Dear List,
  Sorry, I attached a wrong sessionInfo() to my last e-mail (below). It should be:
  > sessionInfo()
R version 2.4.1 (2006-12-18) 
i386-pc-mingw32 
  locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
  attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
  other attached packages:
barley1cdf      limma       affy     affyio    Biobase 
  "1.14.0"   "2.9.13"   "1.12.2"    "1.2.0"   "1.12.2" 
   
  Looking forward to hearing your comments,
  Lev.

Lev Soinov <lev_embl1@yahoo.co.uk> wrote:
  Hi James, List,
My previous e-mail was bounced because of the attachment, so i decided to send it without the one this time.
This is related to my previous questions about barley1.cdf.

I do not have any evidence for mistakes in barley1.cdf (I do not have ANY experience in making CDFs). However, I am getting a little bit strange results second time in a row. I have e-mailed to the list some time ago about Barley arrays and paired design in LIMMA. The thing was that I was getting only upregulated genes in the expreiment. Gordon kindly helped to conclude that the results were genuine/correct. But now I am analysing a new dataset with the same amount of data (3 pairs of barley arrays, 6 arrays in total), I am using the same scripts as before (as described in the LIMMA user guide, p.40, for paired design), below. The script is very simple and is exactly as in the user guide. And once again I am getting only upregulated genes, no downregulation at all.
This time I have a different treatment and it seems VERY strange that there is no downregulated genes at all again. Therefore I started to suspect some mistake in the cdf environment.

Thank you very much for all your help!
Lev.

memory.limit(size = 2048)
data<-ReadAffy()
temp<-rma(data)
targets <- readTargets("Targets.txt")
Pair <- factor(targets$Pair)
Treat <- factor(targets$Treatment, levels=c("A","B"))
design <- model.matrix(~Pair+Treat)
fit_pair <- lmFit(temp, design)
fit_pair <- eBayes(fit_pair)
topTable(fit_pair, coef="TreatB")

Targets file:
FileName Pair Treatment
1.CEL 1 A
2.CEL 1 B
3.CEL 2 A
4.CEL 2 B
5.CEL 3 A
6.CEL 3 B

> sessionInfo()
R version 2.4.1 (2006-12-18) 
i386-pc-mingw32 
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
attached base packages:
[1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" 
other attached packages:
mouse4302cdf limma affy affyio Biobase 
"1.5.1" "2.9.8" "1.12.2" "1.2.0" "1.12.2" 



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