need help for t.test using "by"

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need help for t.test using "by"

1Rnwb
I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))". when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this
> by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))
Error in t.test.formula(IL1Ra ~ Group, data = .sub) :
  grouping factor must have exactly 2 levels


I checked my data file and the plate ID has "P16-P47" and the disease column is "Y/N". I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong.
for more detail i amm posting a part of my data.

SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4
1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43
2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36
3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52
4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04
5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36
6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75
7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69
8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61
9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72
10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08
11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29
12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6
13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39
14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15
15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49
16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21
17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27
18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89
19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15
20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86
21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47
22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12
23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78
24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62
25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14
26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 15962.05
27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95
28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39
29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48
30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83
31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02
32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84
33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36
34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61
35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9
36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27
37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77
38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58
39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94
40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11
41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98
42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03
43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89
44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33
45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59
46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49
47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32
48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95
49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6
50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98
51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4
52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42
53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46
54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32
55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11
56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59
57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34
58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27
59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16 111361.43
60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04 12258.96
61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67
62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86
63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88
64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22
65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62
66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66
67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68
68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07
69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68
70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58
71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39
72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01
73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13
74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9
75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23
76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82


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Re: need help for t.test using "by"

1Rnwb
any one
1Rnwb wrote
I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))". when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this
> by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))
Error in t.test.formula(IL1Ra ~ Group, data = .sub) :
  grouping factor must have exactly 2 levels


I checked my data file and the plate ID has "P16-P47" and the disease column is "Y/N". I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong.
for more detail i amm posting a part of my data.

SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4
1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43
2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36
3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52
4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04
5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36
6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75
7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69
8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61
9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72
10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08
11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29
12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6
13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39
14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15
15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49
16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21
17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27
18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89
19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15
20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86
21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47
22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12
23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78
24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62
25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14
26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 15962.05
27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95
28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39
29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48
30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83
31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02
32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84
33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36
34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61
35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9
36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27
37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77
38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58
39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94
40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11
41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98
42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03
43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89
44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33
45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59
46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49
47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32
48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95
49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6
50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98
51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4
52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42
53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46
54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32
55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11
56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59
57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34
58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27
59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16 111361.43
60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04 12258.96
61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67
62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86
63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88
64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22
65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62
66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66
67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68
68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07
69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68
70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58
71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39
72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01
73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13
74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9
75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23
76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82

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Re: need help for t.test using "by"

David Winsemius

On Aug 19, 2009, at 9:00 AM, 1Rnwb wrote:

>
> any one

I looked at your posting yesterday and could not figure out what your  
statistical question was, nor could I figure out how the t.test  
formula related to the column names in the data.frame. I saw no Group  
or IL1Ra variables in your data. I also tried to import that data and  
found that you had more column headers than columns. I gave up.

--
DW

>
> 1Rnwb wrote:
>>
>> I am trying to do ttest for each plate which has equal number of  
>> disease
>> and controls. by searching this forum I found one posting  
>> suggesting OP to
>> use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))".  
>> when i
>> modified this for my use I used to get the pvalues for each plate,
>> recently upgraded to R2.9.x and now i am getting following error  
>> when i
>> use this
>>> by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))
>> Error in t.test.formula(IL1Ra ~ Group, data = .sub) :
>>  grouping factor must have exactly 2 levels
>>
>> I checked my data file and the plate ID has "P16-P47" and the disease
>> column is "Y/N". I have search all but could not locate the answer.  
>> Can
>> anyone suggest me the direction where i am going wrong.
>> for more detail i amm posting a part of my data.
>>
>> SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4
>> 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43
>> 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36
>> 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52
>> 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04
>> 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36
>> 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75
>> 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69
>> 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61
>> 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72
>> 10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08
>> 11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29
>> 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6
>> 13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39
>> 14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15
>> 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49
>> 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99
>> 41823.21
>> 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27
>> 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89
>> 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15
>> 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86
>> 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47
>> 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12
>> 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78
>> 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62
>> 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14
>> 26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25
>> 15962.05
>> 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95
>> 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39
>> 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48
>> 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83
>> 31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02
>> 32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84
>> 33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36
>> 34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83
>> 19587.61
>> 35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9
>> 36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27
>> 37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77
>> 38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32
>> 248857.58
>> 39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94
>> 40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11
>> 41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98
>> 42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03
>> 43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89
>> 44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33
>> 45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59
>> 46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49
>> 47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32
>> 48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95
>> 49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6
>> 50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98
>> 51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4
>> 52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42
>> 53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46
>> 54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32
>> 55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11
>> 56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59
>> 57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34
>> 58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27
>> 59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16
>> 111361.43
>> 60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04
>> 12258.96
>> 61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67
>> 62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86
>> 63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88
>> 64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22
>> 65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62
>> 66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66
>> 67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68
>> 68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07
>> 69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68
>> 70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58
>> 71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39
>> 72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01
>> 73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13
>> 74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9
>> 75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23
>> 76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82
>>
>>
>>
>>
>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: need help for t.test using "by"

1Rnwb
In reply to this post by 1Rnwb
Thanks for the reply, and sorry for not being clear, I have ELISA data for 50 plates, equal number of disease and control samples are located on each plates. I need to do the ttest between each proteins listed as prt1, prt2... prt50 on all the plates 1-50, however for some proteins i have data for 40 plates and that is creating the problem for me when I run   "by(eo,eo$PlateID, function(.sub) t.test(prt1~Disease,data=.sub))". If i only take the data for 40 plates, this command works, unfortunately I do not want to make multiple copies of the same data over to do things. Similarly"by(eo,eo$sex,function(.sub) t.test(prt1~Disease,data=.sub))" is also not working when I select the data for 40 plates. I used these two formulas earlier sucessfully. I am uploading a part of data as a delim file for sampler..txt. Thanks
1Rnwb wrote
any one
1Rnwb wrote
I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))". when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this
> by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))
Error in t.test.formula(IL1Ra ~ Group, data = .sub) :
  grouping factor must have exactly 2 levels


I checked my data file and the plate ID has "P16-P47" and the disease column is "Y/N". I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong.
for more detail i amm posting a part of my data.

SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4
1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43
2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36
3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52
4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04
5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36
6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75
7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69
8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61
9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72
10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08
11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29
12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6
13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39
14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15
15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49
16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21
17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27
18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89
19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15
20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86
21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47
22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12
23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78
24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62
25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14
26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 15962.05
27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95
28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39
29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48
30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83
31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02
32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84
33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36
34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61
35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9
36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27
37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77
38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58
39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94
40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11
41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98
42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03
43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89
44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33
45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59
46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49
47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32
48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95
49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6
50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98
51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4
52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42
53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46
54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32
55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11
56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59
57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34
58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27
59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16 111361.43
60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04 12258.96
61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67
62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86
63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88
64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22
65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62
66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66
67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68
68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07
69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68
70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58
71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39
72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01
73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13
74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9
75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23
76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82