Hi!

I've just started too learnhow to do a microarray analyses.

My data is already in log2, does it mean that its already normalized?

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM803742

How do i continue if I want to do enrichment analyses

If my data is not in log2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM803742  is it rma wich converts it too log2 like this:

> norm <- rma(raw); expr <- exprs(norm);
>Pda <- fitPLM(raw, model = PM ~ -1 + probes + samples)

Thanks,

Anna

dear Anna,

according to the information on GEO the data is already normalized (by RMA) and the values are in log2 scale.

yes, assuming that raw is an AffyBatch object (i.e. was generated by the ReadAffy function from the affy package, which reads the raw Affymetrix CEL files), you can perform the pre-processing using norm <- rma( raw ) . After that you can access the pre-processed expression values (which are in log2 scale) using exprs( norm ).

I suggest to read the vignettes from the affy package as a starting point:

library( affy )

openVignette( "affy" )

Concerning enrichment analysis, if you ment to do a category enrichment analysis: check GOstats package

library( GOstats )

openVignette( "GOstats" )

but before that you eventually want to identify differentially expressed genes, where I suggest to read the limma user guide:

library( limma )

limmaUsersGuide()

I hope this information was somewhat helpful.

cheers, jo

dear Jo,

Thank you very much!!

Anna