Hi!

Please comment if I'm doing anything wrong in these basic codes as the final
list of differentially expressed genes doesn't come up with the gene IDs !!
----

> library(arrayQuality)



> files <- c("B1a.gpr", "B1b.gpr", "B1cDS.gpr")



> TargetInfo <- read.marrayInfo ("targets111.txt")



> mraw <- read.GenePix (files, name.Gb = NULL, name.Rb = NULL,
targets=TargetInfo)



> maQualityPlots(mraw)



> normdata <- maNorm (mraw)



> write.marray (normdata, file="Normalizaed Log-ratios.xls")
# #  library (convert) ;   mdata <- as (normdata, "exprSet")



> LMres <- lmFit (normdata, design = c(1,1,-1),weights=NULL)



> LMres <- eBayes (LMres)



> restable <- toptable (LMres, number = 10, resort.by = "M")



> table2html (restable,filename = "Top 10 D.E. geneList.html", disp="file")



> sessionInfo ()

R version 2.6.0 (2007-10-03)

i386-pc-mingw32



locale:

LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_MONETARY=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252



attached base packages:

 [1] grid      tools     stats     graphics  grDevices datasets  tcltk
utils     methods   base



other attached packages:

 [1] arrayQuality_1.14.0 RColorBrewer_1.0-2  gridBase_0.4-3
hexbin_1.12.0       lattice_0.17-6      convert_1.14.0      Biobase_1.16.3


 [8] marray_1.16.0       limma_2.12.0        svSocket_0.9-5
svIO_0.9-5
R2HTML_1.58         svMisc_0.9-5        svIDE_0.9-5



loaded via a namespace (and not attached):

[1] rcompgen_0.1-17



Regards,
Chintanu

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