[BioC] another question

Naomi Altman naomi at stat.psu.edu
Thu Jul 20 19:17:21 CEST 2006

For this type of problem, it usually helps if you paste your code to 
the end of the message.


At 02:16 PM 7/19/2006, milesg at bu.edu wrote:
>To those who responded to my last e-mail, thanks for the help. I had another
>question. I got my 2 color time course data into limma. I have a targets file
>with 2 replicates per time point for time points 1 day, 2 day, 4 day, 7 day,
>and 14 day. I have LIMMA assuming that these are not ALL replicates 
>by telling
>it so. Please not that any semicolons coming up are NOT part of the code.
>There is supposed to be a nicely sized shift in differential 
>expression from 4
>days to 7 days, so I used those points for my comparison. As the LIMMA manual
>has stated, I have assigned my levels variable lev, assigned my factors
>variable f, and my design. I made my colnames variable: 
>colnames(design)=lev ;
>and my fit variable: fit=lmFit(MA, design); where MA is the normalized RG. I
>continue to follow the manual (the variable names it gave me were X1day,
>X2day, etc.): cont=makeContrasts("X7day-X4day", levels=design); I then did
>fit2=contrasts.fit(fit, cont) ; then fit2=eBayes(fit2); then I did
>selected=p.adjust(fit2$F.p.value, method="BH")<0.05 to get the genes that
>change from 4 days to 7 days with strong p-values. Unfortunately, looking at
>the results yield only about 30 genes (there should be several hundred), none
>of whom (by eye) undergo any significant change in differential expression
>from the 4 day point to the 7 day point. Can someone please help me with what
>I may be doing wrong? Any help would be greatly appreciated. Thanks!
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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