Hi, I have an unidentied error in the gcrma package. I'm stuck on the cause: > gcrma.cold.control <- gcrma(raw.cold.control) Computing affinities.Done. Adjusting for optical effect........................................................Done. Adjusting for non-specific binding........................................................Done. Normalizing Calculating Expression Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from an object of a basic class ("NULL") with no slots The raw.cold.control object is: AffyBatch object size of arrays=712x712 features (221801 kb) cdf=ATH1-121501 (22810 affyids) number of samples=56 number of genes=22810 annotation=ath1121501 notes=Merge from two AffyBatches with notes: 1) Merge from two AffyBatches with notes: 1) Merge from two AffyBatches with notes: 1) , and 2) , and 2) , and 2) R version 2.0.1 gcrma versionl 1.1.3 I would really appreciate some feedback on the possible cause of the errors. Dion Whitehead -- *************************** Dion Whitehead Division of Bioinformatics The Westfalian Wilhelms University of Muenster Botanical Institute, Schlossplatz 4 D48149 Muenster Germany Phone: +49-251-83-21633 Fax: +49-251-83-21631 http://www.uni-muenster.de/Biologie.Botanik/ebb/

can you try rma and see if you get error too? rma.cold.control <- rma(raw.cold.control) from your output it seems upto normalizing it is working OK. After that the function is the same as rma and actually calls rma to calculate expression. best, Jean On Fri, 11 Feb 2005, Dion Whitehead wrote: > Hi, > > I have an unidentied error in the gcrma package. I'm stuck on the cause: > > > gcrma.cold.control <- gcrma(raw.cold.control) > Computing affinities.Done. > Adjusting for optical > effect........................................................Done. > Adjusting for non-specific > binding........................................................Done. > Normalizing > Calculating Expression > Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from > an object of a basic class ("NULL") with no slots > > > The raw.cold.control object is: > AffyBatch object > size of arrays=712x712 features (221801 kb) > cdf=ATH1-121501 (22810 affyids) > number of samples=56 > number of genes=22810 > annotation=ath1121501 > notes=Merge from two AffyBatches with notes: 1) Merge from two > AffyBatches with notes: 1) Merge from two AffyBatches with notes: 1) , > and 2) , and 2) , and 2) > > R version 2.0.1 > gcrma versionl 1.1.3 > > I would really appreciate some feedback on the possible cause of the errors. > > Dion Whitehead > > -- > *************************** > Dion Whitehead > Division of Bioinformatics > The Westfalian Wilhelms University of Muenster > Botanical Institute, Schlossplatz 4 > D48149 Muenster > Germany > > Phone: +49-251-83-21633 > Fax: +49-251-83-21631 > http://www.uni-muenster.de/Biologie.Botanik/ebb/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi, I have an unidentied error in the gcrma package. I'm stuck on the cause: > gcrma.cold.control <- gcrma(raw.cold.control) Computing affinities.Done. Adjusting for optical effect........................................................Done. Adjusting for non-specific binding........................................................Done. Normalizing Calculating Expression Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from an object of a basic class ("NULL") with no slots The raw.cold.control object is: AffyBatch object size of arrays=712x712 features (221801 kb) cdf=ATH1-121501 (22810 affyids) number of samples=56 number of genes=22810 annotation=ath1121501 notes=Merge from two AffyBatches with notes: 1) Merge from two AffyBatches with notes: 1) Merge from two AffyBatches with notes: 1) , and 2) , and 2) , and 2) R version 2.0.1 gcrma versionl 1.1.3 I would really appreciate some feedback on the possible cause of the errors. Dion Whitehead -- *************************** Dion Whitehead Division of Bioinformatics The Westfalian Wilhelms University of Muenster Botanical Institute, Schlossplatz 4 D48149 Muenster Germany Phone: +49-251-83-21633 Fax: +49-251-83-21631