how to normalize microarray expression set

Question

[Michel Edwar]

I have downloaded a database from GEO using getGEO and then converted it into ExpressionSets using GDS2eSet. Now I am trying to normalize it using rma. It gives me error :unable to find an inherited method for function ‘probeNames’ for signature ‘"ExpressionSet". Which function I showed use to normalize the expression set ?

a1<-getGEO('GDS4758',  destdir=".")
eset<- GDS2eSet(a1, do.log2=TRUE)
eset1<-rma(eset)

[Diwan]

The platform for GDS4758 is GENE ST array. For ST array normalization 'oligo' package is used. So e.rempel's suggestion below should work. Check this webpage http://homer.ucsd.edu/homer/basicTutorial/affymetrix.html (see "Newer Affymetrix Arrays (Gene ST arrays, etc.")

Answer 1

[e.rempel]

Hi,

the error message resembles one in this thread. It looks like you should use different rma function, namely from oligo package. You could try oligo::rma instead of rma (after possible installation of oligo library)

[Kevin Blighe]

Indeed, for ST arrays, you should use the oligo package, not affy