[BioC] Question about affy

Rafael A. Irizarry rafa@jhu.edu
Wed, 15 May 2002 11:00:33 -0400 (EDT)


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
> 
> 
> 
> 
> 
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