[BioC] Limma and negative p-values

[Ovokeraye Achinike-Oduaran]

Hi all,

Sorry...a recall of my previous mail...the p-values are fine(or not)
but not negative...the corrected p-values, however, look very shady.
Any suggestions there?

Thanks

On Thu, Mar 15, 2012 at 3:46 PM, Ovokeraye Achinike-Oduaran
<ovokeraye at gmail.com> wrote:
> 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