[BioC] F p.value.adj missing from write.fit/limma

James W. MacDonald jmacdon at uw.edu
Thu Mar 29 15:51:20 CEST 2012

Hi Pascal,

On 3/29/2012 9:20 AM, Pascal Gellert wrote:
> Dear Bioconductor members,
> I am using limma to analyze my microarrays. Therefore I apply lmFit 
> and eBayes on my normalized data. Finally I write the result to a text 
> file by write.fit function. For multiple testing correction I chose 
> adjust='fdr' in the write.fit function. Usually everything works just 
> as it should. However in some cases, the result file does not contain 
> the column "F p.value.adj". The columns with the adjusted p-values 
> ("p.value.adj") and p-value for the F-statistic ("F p.value") are 
> present.
> Obviously I am doing something wrong, but I cannot figure out what it 
> is since I am using exactly the same code for different data sets and 
> the "F p.value.adj" column does not show up for one data set only.
> Thanks for your help,
> Pascal
> R version 2.10.1 (2009-12-14)
> limma_3.2.3

You need to do two things first. One, update to a current version of R. 
Two, give a small, reproducible code example.



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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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