Hello,

I am using justRMA for processing 350 CEL files. When I does with RMA I get
34901 probe intensities  which match the CDF file. However, when I run
justRMA, I get only 23068 probe intensities. I am not sure why would this
happen?

Below is the code I am using:

library(affy)
   setwd('/home/run/testcel')
    expr.vals <- justRMA(cdfname = "primeviewhsrefseqcdf")
    write.exprs(expr.vals, file= 'Customoutput.csv', sep=",", row.names=F,
col.names=T, quote=F)

Could you please advise me here on how to modify the script so that I
get normalized probe intensities for all the  probe sets?

Thank you for your attention and time.

Bhargavi

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