[BioC] ExpressionSet created by procset method in ArrayExpress

[Md.Mamunur Rashid]

Dear Martin,
Thanks for your prompt reply. The work around you mentioned worked. I am 
trying to do some background correction, quality control, normalisation 
and gene annotation of the data. I have read the reference manula of 
lumi package and it seems to provide all those features. So I was 
wondering is there any way I can convert the ExpressionSet object 
LumiBatch object to apply the lumi methods on them. I still dont have 
much idea about the limma packge. I have started reading it. I will be 
obliged if you can provide me with any suggestion. Thanks again for you 
help.

regards,
Mamun

Martin Morgan wrote:
> 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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>
>