[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
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
> 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,
> R version 2.10.1 (2009-12-14)
You need to do two things first. One, update to a current version of R.
Two, give a small, reproducible code example.
> Bioconductor mailing list
> Bioconductor at r-project.org
> Search the archives:
James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
More information about the Bioconductor