Hi, I'm using the affy package to read in data from 6 MG_U74A chips. This is my first time, so I'm trying to replicate the steps in affy.pdf. The data seems to be read in properly, and pm, mm, boxplot, normalize all seem to work on the whole object. However, any attempt to take subsets of the object itself fails: > Data <- ReadAffy() > Data[1,] Error in checkSlotAssignment(object, name, value) : Value supplied is not valid for slot "pData", is(value, "data.frame") is not TRUE > Data[,1] Error in checkSlotAssignment(object, name, value) : Value supplied is not valid for slot "pData", is(value, "data.frame") is not TRUE Any pointers on what might be causing this ? Deepayan ---------------------------------------------------- P.S.: In case it helps, here's some more output: > Data <- ReadAffy() reading CDF file processing information reading 6 CEL files...... preparing probe level object > Data Plob object CDF used=MG_U74A.cdf number of chips=6 number of genes=12654 number of probe pairs=201964 annotation= description= notes= size of chip=640x640 chip names= aged0-1 aged0-2 aged0-3 young0-1 young0-2 young0-3 > pm(Data)[1:5,] aged0-1 aged0-2 aged0-3 young0-1 young0-2 young0-3 97180_f_at12 15687.0 14791.0 17047.0 15903.8 16362.0 13671.0 97368_at10 18634.0 14839.3 19023.0 18568.0 20432.0 16068.0 97579_f_at8 5508.8 5069.8 5572.8 6346.0 7474.5 5642.5 95664_at5 6101.0 4624.3 6912.0 7200.0 7652.0 6821.0 101287_s_at5 1526.0 1336.3 1505.0 1993.0 1835.0 1774.0 > mm(Data)[1:5,] aged0-1 aged0-2 aged0-3 young0-1 young0-2 young0-3 97180_f_at12 10309.8 10016.0 10891.0 13610.3 13646.0 11988.0 97368_at10 6745.3 5097.0 6346.3 9579.0 7937.0 6944.0 97579_f_at8 3165.5 2809.0 3509.8 4360.0 4396.3 3580.8 95664_at5 3557.0 2729.0 3972.5 5056.5 4385.0 4197.0 101287_s_at5 962.8 836.8 1059.5 1294.0 1160.0 1492.0 __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com

this is a bug. we assume that you will provide phenoData (look at the help file or the Biobase description). if you have phenotypic data and it has more than 2 covariantes add it. that will solve your problem. otherwise, while we fix it, here is a work around n <- 6 ## number of samples pdata <- data.frame(tmp1=1:n,tmp2=1:n) varlabels <- list("tmp1: so it works","tmp2: so it works") phenodata <- new("phenoData",pData=pdata,varLabels=varlabels) Data <- ReadAffy(phenodata=phenodata) then continue... thanks for finding the bug. also for making us relize we need to say we recommend usinge phenoData in the documentation. Rafael thanks for finding this.On Wed, 15 May 2002, Deepayan Sarkar wrote: > > Hi, > > I'm using the affy package to read in data from 6 MG_U74A chips. > This is my first time, so I'm trying to replicate the steps in > affy.pdf. The data seems to be read in properly, and pm, mm, > boxplot, normalize all seem to work on the whole object. > > However, any attempt to take subsets of the object itself fails: > > > Data <- ReadAffy() > > Data[1,] > Error in checkSlotAssignment(object, name, value) : > Value supplied is not valid for slot "pData", is(value, "data.frame") is not > TRUE > > Data[,1] > Error in checkSlotAssignment(object, name, value) : > Value supplied is not valid for slot "pData", is(value, "data.frame") is not > TRUE > > Any pointers on what might be causing this ? > > Deepayan > > ---------------------------------------------------- > P.S.: In case it helps, here's some more output: > > > > Data <- ReadAffy() > reading CDF file > processing information > reading 6 CEL files...... > preparing probe level object > > > > Data > Plob object > CDF used=MG_U74A.cdf > number of chips=6 > number of genes=12654 > number of probe pairs=201964 > annotation= > description= > notes= > size of chip=640x640 > chip names= > aged0-1 > aged0-2 > aged0-3 > young0-1 > young0-2 > young0-3 > > > > pm(Data)[1:5,] > aged0-1 aged0-2 aged0-3 young0-1 young0-2 young0-3 > 97180_f_at12 15687.0 14791.0 17047.0 15903.8 16362.0 13671.0 > 97368_at10 18634.0 14839.3 19023.0 18568.0 20432.0 16068.0 > 97579_f_at8 5508.8 5069.8 5572.8 6346.0 7474.5 5642.5 > 95664_at5 6101.0 4624.3 6912.0 7200.0 7652.0 6821.0 > 101287_s_at5 1526.0 1336.3 1505.0 1993.0 1835.0 1774.0 > > > > mm(Data)[1:5,] > aged0-1 aged0-2 aged0-3 young0-1 young0-2 young0-3 > 97180_f_at12 10309.8 10016.0 10891.0 13610.3 13646.0 11988.0 > 97368_at10 6745.3 5097.0 6346.3 9579.0 7937.0 6944.0 > 97579_f_at8 3165.5 2809.0 3509.8 4360.0 4396.3 3580.8 > 95664_at5 3557.0 2729.0 3972.5 5056.5 4385.0 4197.0 > 101287_s_at5 962.8 836.8 1059.5 1294.0 1160.0 1492.0 > > > > > > __________________________________________________ > Do You Yahoo!? > LAUNCH - Your Yahoo! Music Experience > http://launch.yahoo.com > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >