[BioC] ExpressionSet created by procset method in ArrayExpress

[Martin Morgan]

Md.Mamunur Rashid wrote:
> Hi everyone,
> 
> I have recently posted a query names "How to use ExpressionSet for
> further
> Analysis"(http://article.gmane.org/gmane.science.biology.informatics.conductor/24343/match=use+expressionset+further+analysis)
> 
> 
> 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
> procset
>> 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.

Hi Mamun -- this seems to be a problem with ArrayExpress (running
example(getAE) produces an ExpressionSet like you describe, too).

A work-around is

  m <- exprs(p1)
  mode(m) <- "numeric"
  exprs(p1) <- m

Your first question in your earlier post was

  1. Now I am not sure how can I use this ExpressionSet object for
     further analysis of the Data?

but you need to be more specific about what you'd like to do next --
qa/qc, differential expression (limma), clustering, gene set analysis, ...

Martin

> 
> regards,
> Mamun
> 
> 
> 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])
> 
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