[BioC] extract intensity values from AffyBatch

[Paul Geeleher]

Maybe you could use the expresso() function from the affy library and
only do the summarization step (i.e. skip normalization background
correction etc). Should give you what I *think* you're looking for.

Paul.

On Wed, May 18, 2011 at 11:22 AM, Saurabh Bundela
<saurabh.bundela at gmail.com> wrote:
> Hi,
>
> Well I am not very sure, how to get exactly get it.... However you can get
> probe level intensity data (Perfect match and Mis-match probes) using affy
> methods like probes, pm, mm etc.
>
> Please try this code
>
> data<-ReadAffy()
> pm<-as.data.frame(probes(data,which="pm"))
> mm<-as.data.frame(probes(data,which="mm"))
> names(pm)[1]<-"ProbesetID"
> names(mm)[1]<-"ProbesetID"
> write.table(pm,"PM.txt",sep="\t")
> write.table(mm,"MM.txt",sep="\t")
>
> This should give two files with probe intensities from perfect match and mis
> match probes, hope it'll be useful
>
> Best Regards,
>
> Saurabh
>
>
> On Wed, May 18, 2011 at 3:10 PM, Assa Yeroslaviz <frymor at gmail.com> wrote:
>
>> Hi,
>>
>> thanks for the response. Unfortunately this wasn't what I meant.
>> I know about the way of extracting the normalized data. What I want is the
>> raw data values for each of the probes on a probes set.
>>
>> Assa
>>
>> On Wed, May 18, 2011 at 10:31, Saurabh Bundela <saurabh.bundela at gmail.com>wrote:
>>
>>> Hi,
>>>
>>> I think you can first convert AffyBatch obejct into ExpressionSet data
>>> type (by using preprocessing algorithms like rma, plier, gcrma etc) and than
>>> by using method 'exprs' you should get full matrix with probe names....
>>>
>>> >>>sample code
>>>
>>> library(affy)
>>> #Import cel files into R
>>> data<-ReadAffy()
>>> #preprocess AffyBatch object 'data' with RMA
>>> data2<-rma(data)
>>> #extracting matrix
>>> data3<-exprs(data2)
>>> #converting matrix to data frame
>>> data4<-as.data.frame(data3)
>>> names(data4)[1]<-"ProbesetID"
>>> #exporting data matrix to external tab-delimited file for downstream
>>> analysis
>>> write.table(data4,"Data.txt",sep="\t")
>>> <<<<<<
>>>
>>>
>>> Best Regards,
>>>
>>> Saurabh
>>>
>>> On Wed, May 18, 2011 at 1:16 PM, Assa Yeroslaviz <frymor at gmail.com>wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm trying to extract a matrix of intensity values from an AffyBatch
>>>> object.
>>>>
>>>> I know I can have them using
>>>> > Intensity(AffyBatch)
>>>> or
>>>> >exprs(AffyBatch)
>>>>
>>>> but I would like to have a full matrix with the probe names.
>>>> Unfortunately I can't find a way of doing it.
>>>>
>>>> There are several way of extracting the names of the probes, but not in
>>>> the
>>>> same order or magnitude compared to the intensity array.
>>>>
>>>> > length(geneNames(rawData))[1] 18952> length(probeNames(rawData))[1]
>>>> 265358> dim(intensity(rawData))[1] 535824     12> dim(exprs(rawData))[1]
>>>> 535824     12
>>>>
>>>> Does anyone has an idea of how to extract these Values into a matrix. I
>>>> have
>>>> the original CEL files.
>>>>
>>>> Even a way outside of R will be welcome.
>>>>
>>>> Thanks
>>>>
>>>> Assa
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
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>>>
>>>
>>
>
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>
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-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com