[BioC] Limma and negative p-values

[Ovokeraye Achinike-Oduaran]

Hi all,

Trying to use limma(code below) to do some DE analysis...and I get
negative p-values. Not quite sure where I went wrong here...please
help!

Thanks.

Avoks.

gds158dat = getGEO('GDS158',destdir=".")
gds158eset = GDS2eSet(gds158dat, do.log2=TRUE)
groups= pData(gds158eset)$metabolism
groups=as.character(groups)
groups[groups=="insulin sensitive"]= "IS"
groups[groups=="insulin resistant"]= "IR"
f = factor(groups, levels=c("IS","IR"))
design_gds158 = model.matrix(~0+f)
colnames(design_gds158) = levels(f)
cont.matrix = makeContrasts(IR-IS, levels=design_gds158)
fit=lmFit(gds158eset, design_gds158)
fit2 = contrasts.fit(fit, cont.matrix)
fit2 = eBayes(fit2)
results = topTable(fit2, adjust ="BH", number = nrow(gds158eset))

sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_xxx.1252  LC_CTYPE=English_xxx.1252
[3] LC_MONETARY=xxx.1252 LC_NUMERIC=C
[5] LC_TIME=xxx.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ArrayExpress_1.14.0 GEOquery_2.20.8     limma_3.10.2
 [4] XML_3.9-4.1         RCurl_1.91-1.1      bitops_1.0-4.1
 [7] puma_2.6.0          mclust_3.4.11       affy_1.32.1
[10] Biobase_2.14.0

loaded via a namespace (and not attached):
[1] affyio_1.22.0         BiocInstaller_1.2.1   preprocessCore_1.16.0
[4] tools_2.14.1          zlibbioc_1.0.0