Affy Package

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Affy Package

Vallejo, Roger
Dear R Users,
In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best:

bgcorrect.metod = rma rma2 mas

normalize.method = qspline quantiles loess

pmcorrect.method = pmonly subtractmm mas

summary.method = liwong avgdiff medianpolish mas

There are many options within each method. I would appreciate a hint on the best combination.
Thank you very much in advance.
Roger
 
Roger L. Vallejo, Ph.D.
Computational Biologist & Geneticist
U.S. Department of Agriculture, ARS
National Center for Cool & Cold Water Aquaculture
11861 Leetown Road
Kearneysville, WV 25430
Voice:  (304) 724-8340 Ext. 2141
Email:  [hidden email]
http://www.ars.usda.gov/pandp/people/people.htm?personid=37662

        [[alternative HTML version deleted]]

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Affy Package

Vallejo, Roger
Dear R Users,
In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best:

bgcorrect.metod = rma rma2 mas

normalize.method = qspline quantiles loess

pmcorrect.method = pmonly subtractmm mas

summary.method = liwong avgdiff medianpolish mas

There are many options within each method. I would appreciate a hint on the best combination.
Thank you very much in advance.
Roger
 
 
Roger L. Vallejo, Ph.D.
Computational Biologist & Geneticist
U.S. Department of Agriculture, ARS
National Center for Cool & Cold Water Aquaculture
11861 Leetown Road
Kearneysville, WV 25430
Voice:  (304) 724-8340 Ext. 2141
Email:  [hidden email]
http://www.ars.usda.gov/pandp/people/people.htm?personid=37662

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
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: Affy Package

Uwe Ligges


Vallejo, Roger wrote:

> Dear R Users,
> In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best:
>
> bgcorrect.metod = rma rma2 mas
>
> normalize.method = qspline quantiles loess
>
> pmcorrect.method = pmonly subtractmm mas
>
> summary.method = liwong avgdiff medianpolish mas
>
> There are many options within each method. I would appreciate a hint on the best combination.


There is more than one implemented, hence we can guess that there is no
generally best one among these, i.e. it depends on your data what to use.

Uwe Ligges


> Thank you very much in advance.
> Roger
>  
>  
> Roger L. Vallejo, Ph.D.
> Computational Biologist & Geneticist
> U.S. Department of Agriculture, ARS
> National Center for Cool & Cold Water Aquaculture
> 11861 Leetown Road
> Kearneysville, WV 25430
> Voice:  (304) 724-8340 Ext. 2141
> Email:  [hidden email]
> http://www.ars.usda.gov/pandp/people/people.htm?personid=37662
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> 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.

______________________________________________
[hidden email] mailing list
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: Affy Package

Uwe Ligges
Damn, this was a cross-post (and I replied to all), apologies for my
re-cross-posting.

To Roger, the original poster: PLEASE do read the posting guide of
R-help before posting and NEVER EVER do crossposting again.

Thanks,
Uwe Ligges

Uwe Ligges wrote:

>
>
> Vallejo, Roger wrote:
>> Dear R Users,
>> In the expresso function, which combination of these methods for data
>> pre-processing (when using affymetrix oligo arrays) is the best:
>>
>> bgcorrect.metod = rma rma2 mas
>>
>> normalize.method = qspline quantiles loess
>>
>> pmcorrect.method = pmonly subtractmm mas
>>
>> summary.method = liwong avgdiff medianpolish mas
>>
>> There are many options within each method. I would appreciate a hint
>> on the best combination.
>
>
> There is more than one implemented, hence we can guess that there is no
> generally best one among these, i.e. it depends on your data what to use.
>
> Uwe Ligges
>
>
>> Thank you very much in advance.
>> Roger
>>  
>>  
>> Roger L. Vallejo, Ph.D.
>> Computational Biologist & Geneticist
>> U.S. Department of Agriculture, ARS
>> National Center for Cool & Cold Water Aquaculture
>> 11861 Leetown Road
>> Kearneysville, WV 25430
>> Voice:  (304) 724-8340 Ext. 2141
>> Email:  [hidden email]
>> http://www.ars.usda.gov/pandp/people/people.htm?personid=37662
>>
>>     [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list
>> 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.
>

______________________________________________
[hidden email] mailing list
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.