Question: how to normalize microarray expression set
1
gravatar for Michel Edwar
2.6 years ago by
Michel Edwar70
Sweden
Michel Edwar70 wrote:

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)
rma getgeo gds • 1.8k views
ADD COMMENTlink modified 14 months ago by Kevin Blighe60k • written 2.6 years ago by Michel Edwar70

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.")

ADD REPLYlink written 2.6 years ago by Diwan570
1
gravatar for e.rempel
2.6 years ago by
e.rempel820
Germany, Heidelberg, COS
e.rempel820 wrote:

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)

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by e.rempel820

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

ADD REPLYlink written 14 months ago by Kevin Blighe60k
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