Dear list, I get the following error when trying to run affycomp on rma expressions of the hgu133a spike in experiment, > s.rma <-read.newspikein("eset_hgu133a/rma133.csv") > a.rma <-assessSpikeIn2(s.rma,method.name="rma") Performing 3 assessments that will take a few secondsError in exprset[-spikein, ] : only 0's may mix with negative subscripts The command runs smoothly on hgu95a data, though Any help would be greatly appreciated regards, Ariel./ -- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339

my mistake! I did not realize that it was a HG-U133A_tag array, and not a HG-U133A one. There were some control probesets in the former that did not appear in the second one : : AFFX-r2-TagA_at : AFFX-r2-TagB_at : AFFX-r2-TagC_at : AFFX-r2-TagD_at : AFFX-r2-TagE_at : AFFX-r2-TagF_at : AFFX-r2-TagG_at : AFFX-r2-TagH_at Can anyone tell me if this is the only difference between both arrays? thanks, Ariel./ On June 29, 2005 12:34 pm, Ariel Chernomoretz wrote: > affycomp hgu133 assessment error >Dear list, > >I get the following error when trying to run affycomp on rma expressions of >the hgu133a spike in experiment, > > > s.rma <-read.newspikein("eset_hgu133a/rma133.csv") > > a.rma <-assessSpikeIn2(s.rma,method.name="rma") > Performing 3 assessments that will take a few secondsError in > exprset[-spikein, ] : only 0's may mix with negative subscripts > >The command runs smoothly on hgu95a data, though >Any help would be greatly appreciated >regards, >Ariel./ -- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339