[BioC] question regarding qc function in simpleaffy package

James Anderson janderson_net at yahoo.com
Wed Mar 31 15:31:06 CEST 2010


I am trying to use the qc function in the simpleaffy package to generate those qc metrics for a bunch of cel files in U133A, but I need to use a different cdf file, not the Affy CDF. 

Below is the code

cel.path <- "C:\Cel"
fn <- list.celfiles(cel.path, full.name = T)
raw.data <- ReadAffy(filenames = fn,cdfname = "hgu133ahsentrezg")   
x.mas5 <- call.exprs(raw.data,"mas5",sc = 100)
qcmas5 <- qc(raw.data,x.mas5)

Everything runs smoothly except the last line, it has the following warning message:

Warning message:
In qc.affy(unnormalised, ...) :
  CDF Environment name ' hgu133acdf ' does not match cdfname ' hgu133ahsentrezgcdf '

Is this problem negligible? or it is serious? I've looked into the qc function and it does not seem to have an argument that allows you to specify cdfname. 



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