[BioC] Creating LumiBatch object from ExpressionSet

[Md.Mamunur Rashid]

Dear Martin,

Thanks for your reply.  According to the lumi documentation it extends 
Expression set class. With my limited knowledge about bioconductor I 
assumed there should be a way to convert/adapt an Expressionset object 
to a LumiBatch object. When I tried to create a LumiBatch object from 
the Expression Set object it shows me following error:

 > lumiobj <- new('LumiBatch', exprs = exprs(p1), se.exprs = exprs(p1)) 
// p1 is the ExpressionSet

Error ::   Error in function (storage.mode = c("lockedEnvironment", 
"environment",  :
          'AssayData' elements with invalid dimensions: 'se.exprs'

For the convinient I will briefly state the workflow I am trying to 
inplement below:

*Step 1.* Obtained illumina MicroArray Data from EBI ArrayExpress 
repository

    For testing purpose I have donwloaded the files manually and passed
    them to *"procset"* function of  *ArrayExpress *package of
    bioconductor package and created an ExpressionSet object

*Step 2*. Backgroud correction and Normaliation of Data, *Step 3 
*Annotation and *Step 4 *selection of significantly differentially 
expressed Genes

    Since the bioconductor lumi package provides these functionalities I
    was trying to convert the ExpressionSet object to a LumiBatch object.

I will look forward for any suggestions. Thanks to martin again for 
adding the maintainer of lumi package to the email.

regards,
Md.Mamunur Rashid

Martin Morgan wrote:
> 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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>>>>     
>>>>         
>>>   
>>>       
>
>