[BioC] GEOquery and Limma

[Ovokeraye Achinike-Oduaran]

Hi all,

When running differential expression analysis on Limma with GDS or GSE
data retrieved with GEOquery, what is the right input option: do.log2
= TRUE or do.log2=FALSE? I read in one of the documentations
(http://svitsrv25.epfl.ch/R-doc/library/GEOquery/html/GDS2MA.html)
that to do the conversions:

GDS2MA(GDS,do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE)
GDS2eSet(GDS,do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE

The results are obviously very different from the do.log2=TRUE option.
But the results for logFC from do.log2=FALSE for GDS157, for example,
looks a bit strange. Is there something I'm reading wrongly perhaps?

Please help.

Regards.

Avoks