[BioC] Creating LumiBatch object from ExpressionSet
Md.Mamunur Rashid
mamunur.rashid at kcl.ac.uk
Wed Jul 29 18:07:57 CEST 2009
Dear Pan Du,
Thanks for such a prompt reply. I will try them and give you the
feedback as soon as I can.
regards,
Mamun
Pan Du wrote:
> Hi Md.Mamunur,
>
> As LumiBatch class is inherited from ExpressionSet class, and most functions
> in the lumi package support both ExpressionSet and LumiBatch objects, except
> some functions specifically require additional information included in the
> LumiBatch class. So usually there is no need to force ExpressionSet objects
> as LumiBatch objects.
>
>
> Pan
>
>
> On 7/29/09 10:14 AM, "Md.Mamunur Rashid" <mamunur.rashid at kcl.ac.uk> wrote:
>
>
>> 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.condu
>>>>>> ctor/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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>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>
>
> ------------------------------------------------------
> Pan Du, PhD
> Research Assistant Professor
> Northwestern University Biomedical Informatics Center
> 750 N. Lake Shore Drive, 11-176
> Chicago, IL 60611
> Office (312) 503-2360; Fax: (312) 503-5388
> dupan (at) northwestern.edu
> ------------------------------------------------------
>
>
>
>
>
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