Question: how to normalize microarray expression set
1
gravatar for Michel Edwar
19 months 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 • 1.1k views
ADD COMMENTlink modified 7 weeks ago by Kevin Blighe42k • written 19 months 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 19 months ago by Diwan560
1
gravatar for e.rempel
19 months ago by
e.rempel770
Germany, Heidelberg, COS
e.rempel770 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 19 months ago • written 19 months ago by e.rempel770

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

ADD REPLYlink written 7 weeks ago by Kevin Blighe42k
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