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

Pascal Gellert pascal.gellert at mpi-bn.mpg.de
Thu Mar 29 17:20:58 CEST 2012

Thanks Jim, you are absolutely right. Pasting the code would have 
clearly shown that I did something wrong. Meanwhile I figured out 
myself, that the F p-value gets only corrected with an additional 
parameter like here:

write.fit(fit2, file="file", sep="\t", adjust='fdr', F.adjust='fdr')


On 03/29/2012 03:51 PM, James W. MacDonald wrote:
> 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.
> Best,
> Jim
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