[BioC] ExpressionSet created by procset method in ArrayExpress

[Martin Morgan]

Md.Mamunur Rashid <mamunur.rashid at kcl.ac.uk> writes:

> 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.

Hi Mamun -- I think the workflow you're outlining (from ArrayExpress
to lumi) is different from what either package author envisioned, and
requires some expert knowledge of the internal structure of the data
from both sources. I've added the maintainer of lumi to the email,
perhaps he will have a solution.

Others on the list might have more experience with this.

Martin

> 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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>>
>>   
>

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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