adjusted p value, fdr

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adjusted p value, fdr

anikaM
Hello,

I have a data set which has 15568 entries

I am trying to calculate adjusted p values using p value via:

head(x1g)

                                                   t      P.Value
      adj.P.Val          B       fdr
3TXADqtSkhV1IXRHlg  4.468671 3.072189e-05 0.4782784  1.5253151 0.4782784
34lG83aZ6.WLFnge6s  4.217037 7.518696e-05 0.5852553  0.8660534 0.5852553
oS67lguv5HpU4i6Pvg -3.939182 1.959413e-04 0.9994637  0.1600655 0.9994637
Qpc2sX7gp.W5E2rRS4  3.732914 3.900822e-04 0.9994637 -0.3471331 0.9994637
NqsVOy_yos30cOQRSE -3.673551 4.737810e-04 0.9994637 -0.4902001 0.9994637
B3SDpegGjpdxnvU0S0 -3.665765 4.859528e-04 0.9994637 -0.5088638 0.9994637

x1g$fdr=p.adjust(x1g$P.Value,method="BH")

the fdr values seem unusually high

if I just do it for the first few p values from my x1g data frame:
>pval=c(3.072189e-05,7.518696e-05,1.959413e-04,3.900822e-04)
> p.adjust(pval,method="BH")
[1] 0.0001228876 0.0001503739 0.0002612551 0.0003900822

Can someone please explain what might be the issue.

Thanks
Ana

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Re: adjusted p value, fdr

Jim Lemon-4
Hi Anamarija,
In the first calculation you are implicity using n=15568 as the
default as the number of p values tested.

> p.adjust(pval,method="BH",n=15568)
[1] 0.4782784 0.5852553 1.0000000 1.0000000

If all of your t-tests are related, say by testing the location values
for each row against a fixed value like zero, then this is an
appropriate way to discover whether any differ significantly from your
reference value. In general if you only want to test a subset of the
rows rather than all, you should have a good reason for doing so.

Jim

On Wed, Jan 8, 2020 at 9:15 AM Ana Marija <[hidden email]> wrote:

>
> Hello,
>
> I have a data set which has 15568 entries
>
> I am trying to calculate adjusted p values using p value via:
>
> head(x1g)
>
>                                                    t      P.Value
>       adj.P.Val          B       fdr
> 3TXADqtSkhV1IXRHlg  4.468671 3.072189e-05 0.4782784  1.5253151 0.4782784
> 34lG83aZ6.WLFnge6s  4.217037 7.518696e-05 0.5852553  0.8660534 0.5852553
> oS67lguv5HpU4i6Pvg -3.939182 1.959413e-04 0.9994637  0.1600655 0.9994637
> Qpc2sX7gp.W5E2rRS4  3.732914 3.900822e-04 0.9994637 -0.3471331 0.9994637
> NqsVOy_yos30cOQRSE -3.673551 4.737810e-04 0.9994637 -0.4902001 0.9994637
> B3SDpegGjpdxnvU0S0 -3.665765 4.859528e-04 0.9994637 -0.5088638 0.9994637
>
> x1g$fdr=p.adjust(x1g$P.Value,method="BH")
>
> the fdr values seem unusually high
>
> if I just do it for the first few p values from my x1g data frame:
> >pval=c(3.072189e-05,7.518696e-05,1.959413e-04,3.900822e-04)
> > p.adjust(pval,method="BH")
> [1] 0.0001228876 0.0001503739 0.0002612551 0.0003900822
>
> Can someone please explain what might be the issue.
>
> Thanks
> Ana
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
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Re: adjusted p value, fdr

Yuan Chun Ding
In reply to this post by anikaM
When you do x1g$fdr, you adjusted for  a total of 15568  tests, so FDR is high for those first four entries. When you do p.adjust(pval,method="BH"), you assumed there were only a total of 4 multiple tests in your experiment, so FDR is low.

Ding

-----Original Message-----
From: R-help [mailto:[hidden email]] On Behalf Of Ana Marija
Sent: Tuesday, January 07, 2020 2:18 PM
To: r-help
Subject: [R] adjusted p value, fdr

[Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]

----------------------------------------------------------------------
Hello,



I have a data set which has 15568 entries



I am trying to calculate adjusted p values using p value via:



head(x1g)



                                                   t      P.Value

      adj.P.Val          B       fdr

3TXADqtSkhV1IXRHlg  4.468671 3.072189e-05 0.4782784  1.5253151 0.4782784

34lG83aZ6.WLFnge6s  4.217037 7.518696e-05 0.5852553  0.8660534 0.5852553

oS67lguv5HpU4i6Pvg -3.939182 1.959413e-04 0.9994637  0.1600655 0.9994637

Qpc2sX7gp.W5E2rRS4  3.732914 3.900822e-04 0.9994637 -0.3471331 0.9994637

NqsVOy_yos30cOQRSE -3.673551 4.737810e-04 0.9994637 -0.4902001 0.9994637

B3SDpegGjpdxnvU0S0 -3.665765 4.859528e-04 0.9994637 -0.5088638 0.9994637



x1g$fdr=p.adjust(x1g$P.Value,method="BH")



the fdr values seem unusually high



if I just do it for the first few p values from my x1g data frame:

>pval=c(3.072189e-05,7.518696e-05,1.959413e-04,3.900822e-04)

> p.adjust(pval,method="BH")

[1] 0.0001228876 0.0001503739 0.0002612551 0.0003900822



Can someone please explain what might be the issue.



Thanks

Ana



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PLEASE do read the posting guide https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!4bosaaipAoQGBWeAiIEWMDxU4RRjSCsN0DmyN4DzNZK1NSLhh5pdADDOUx9a$ 

and provide commented, minimal, self-contained, reproducible code.

----------------------------------------------------------------------
------------------------------------------------------------
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This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)

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Re: adjusted p value, fdr

anikaM
Thank you so much for this explanation!

On Tue, Jan 7, 2020 at 4:37 PM Yuan Chun Ding <[hidden email]> wrote:

>
> When you do x1g$fdr, you adjusted for  a total of 15568  tests, so FDR is high for those first four entries. When you do p.adjust(pval,method="BH"), you assumed there were only a total of 4 multiple tests in your experiment, so FDR is low.
>
> Ding
>
> -----Original Message-----
> From: R-help [mailto:[hidden email]] On Behalf Of Ana Marija
> Sent: Tuesday, January 07, 2020 2:18 PM
> To: r-help
> Subject: [R] adjusted p value, fdr
>
> [Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]
>
> ----------------------------------------------------------------------
> Hello,
>
>
>
> I have a data set which has 15568 entries
>
>
>
> I am trying to calculate adjusted p values using p value via:
>
>
>
> head(x1g)
>
>
>
>                                                    t      P.Value
>
>       adj.P.Val          B       fdr
>
> 3TXADqtSkhV1IXRHlg  4.468671 3.072189e-05 0.4782784  1.5253151 0.4782784
>
> 34lG83aZ6.WLFnge6s  4.217037 7.518696e-05 0.5852553  0.8660534 0.5852553
>
> oS67lguv5HpU4i6Pvg -3.939182 1.959413e-04 0.9994637  0.1600655 0.9994637
>
> Qpc2sX7gp.W5E2rRS4  3.732914 3.900822e-04 0.9994637 -0.3471331 0.9994637
>
> NqsVOy_yos30cOQRSE -3.673551 4.737810e-04 0.9994637 -0.4902001 0.9994637
>
> B3SDpegGjpdxnvU0S0 -3.665765 4.859528e-04 0.9994637 -0.5088638 0.9994637
>
>
>
> x1g$fdr=p.adjust(x1g$P.Value,method="BH")
>
>
>
> the fdr values seem unusually high
>
>
>
> if I just do it for the first few p values from my x1g data frame:
>
> >pval=c(3.072189e-05,7.518696e-05,1.959413e-04,3.900822e-04)
>
> > p.adjust(pval,method="BH")
>
> [1] 0.0001228876 0.0001503739 0.0002612551 0.0003900822
>
>
>
> Can someone please explain what might be the issue.
>
>
>
> Thanks
>
> Ana
>
>
>
> ______________________________________________
>
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!Fou38LsQmgU!4bosaaipAoQGBWeAiIEWMDxU4RRjSCsN0DmyN4DzNZK1NSLhh5pdAGPEy5zh$
>
> PLEASE do read the posting guide https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!4bosaaipAoQGBWeAiIEWMDxU4RRjSCsN0DmyN4DzNZK1NSLhh5pdADDOUx9a$
>
> and provide commented, minimal, self-contained, reproducible code.
>
> ----------------------------------------------------------------------
> ------------------------------------------------------------
> -SECURITY/CONFIDENTIALITY WARNING-
>
> This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to r
 eceive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
> ------------------------------------------------------------

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.