[BioC] expresso error
stvjc at channing.harvard.edu
Thu Oct 7 03:36:15 CEST 2010
please provide your sessionInfo() and the specific class of array in
use -- there are various mouse
expression arrays from affy.
On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA
<anjan.purkayastha at gmail.com> wrote:
> I have created an affybatch object from 3 cel files. The files have data
> from Affymetrix's Mouse Expression (Oligonucleotide) array.
> Affybatch object was created by command:
> testAffy <- ReadAffy()
> In the next step I tried to use expresso to adjust background using RMA and
> normalize using loess, using the command:
> testAffy.loess = expresso(testAffy, bgcorrect.method= "rma",
> normalize.method= "loess")
> Here is the output:
> background correction: rma
> normalization: loess
> PM/MM correction :
> expression values:
> background correcting...done.
> normalizing...Done with 1 vs 2 in iteration 1
> Done with 1 vs 3 in iteration 1
> Done with 2 vs 3 in iteration 1
> 1 0.0176947
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "computeExprSet", for
> signature "AffyBatch", "NULL", "NULL"
> The testAffy.loess object was not created. Any idea why I am getting an
> error on running the expresso command?
> Thanks in advance.
> anjan purkayastha, phd.
> research associate
> fas center for systems biology,
> harvard university
> 52 oxford street
> cambridge ma 02138
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