[BioC] ExpressionSet created by procset method in ArrayExpress

Md.Mamunur Rashid mamunur.rashid at kcl.ac.uk
Tue Jul 28 15:34:18 CEST 2009

Hi everyone,

I have recently posted a query names "How to use ExpressionSet for 

I have created an ExpressionSet object using procset method in 
ArrayExpress package.
But the problem I found out that in the ExpressionSet the numeric values 
are in double quote.  (i.e. "123.02".  ) Now when I pass this expression 
set in to the following R code

 > library(lumi)
 > b <- lumiB("p1")    // p1 is the expression set I have created using 
 > MAplot(b)

it shows me an error that Error in log(c("7413.841", "347.639", 
"233.5174", "7120.314", "35.45117",  :  Non-numeric argument to 
mathematical function

can anyone suggest me why the numeric data is converted to 
string/characters while creating ExpressionSet. I will really appriciate 
any help as I am really stuck in this point. Thanks in advance.


below is the code I have used:

> library(ArrayExpress)
 > etabm421 <- list(path = ".",rawadata = NULL, rawfiles = NULL, 
procdata = "E-TABM-421.processed.zip",procfile = 
"E-TABM-421-processed-data-1583036605.txt",sdrf = "E-TABM-421.sdrf.txt", 
idf = "E-TABM-421.idf.txt", adf = "A-MEXP-931.adf.txt")
 > cn = getcolproc(ETABM421)
 > cn
[1] "Reporter REF"              "BeadStudio:AVG_Signal"   
[3] "BeadStudio:Detection Pval"
 > proset = procset(ETABM421,cn[2])

More information about the Bioconductor mailing list