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

On Tue, Oct 18, 2011 at 4:07 AM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > 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? Hi, Avoks. do.log2 when TRUE simply applies a log2 transformation to the data when constructing an MAList or ExpressionSet from the GDS data. It is up to YOU to decide when to perform log2 transformation of GEO data; there is not a "rule" to follow. For GDS157, the data are in GEO as linear intensities. I believe limma assumes that the data have been logged, so doing a log transformation, so log2 transformation is probably appropriate. Sean