[BioC] gcrma problem while processing HuGene-1_0-st-v1 genechip from Affymetrix

[Richard Friedman]

Dear Suparna,

	Both GCRMA and MAS 5 require mismatch probes which are not
on  HuGene-1_0-st-v1, so they cannot be used on this chip.

Best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"School is an evil plot to suppress my individuality"

Rose Friedman, age15










On Jun 11, 2012, at 11:00 AM, suparna mitra wrote:

> Hi,
> I am very new to biocondunctor and microaray. I have limited  
> experience
> with R.
> I am trying to use biocondunctor for analyzing HuGene-1_0-st-v1  
> microarray
> data. I selectected different normalization method (rma, gcrma and  
> mas5).
> For my data rma worked but for for gcrma and mas5 both I have problem.
> For gcrma it gives me a error like: Computing affinitiesError:
> length(prlen) == 1 is not TRUE
>
> And for mas 5 it seems working but I get only a whole list of NA.
>
> Here is what I have done.
>
>> mydata <- ReadAffy()
>> mydata
> AffyBatch object
> size of arrays=1050x1050 features (16 kb)
> cdf=HuGene-1_0-st-v1 (32321 affyids)
> number of samples=18
> number of genes=32321
> annotation=hugene10stv1
>
>> eset <- rma(mydata)
> Background correcting
> Normalizing
> Calculating Expression
>> eset_justrma=justRMA()
>> eset_mas5 <- mas5(mydata)
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...done.
> 32321 ids to be processed
> |                    |
> |####################|
>> eset_gcrma <- gcrma(mydata)
> Adjusting for optical effect..................Done.
> Computing affinitiesError: length(prlen) == 1 is not TRUE   Here is  
> the
> error
>
>> eset_justrma # this worked fine
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 32321 features, 18 samples
>  element names: exprs, se.exprs
> protocolData
>  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st- 
> v1).CEL ...
> MC9_(HuGene-1_0-st-v1).CEL (18 total)
>  varLabels: ScanDate
>  varMetadata: labelDescription
> phenoData
>  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st- 
> v1).CEL ...
> MC9_(HuGene-1_0-st-v1).CEL (18 total)
>  varLabels: sample
>  varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: hugene10stv1
>> eset_mas5 # this seems worked fine but resulted all NA
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 32321 features, 18 samples
>  element names: exprs, se.exprs
> protocolData
>  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st- 
> v1).CEL ...
> MC9_(HuGene-1_0-st-v1).CEL (18 total)
>  varLabels: ScanDate
>  varMetadata: labelDescription
> phenoData
>  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st- 
> v1).CEL ...
> MC9_(HuGene-1_0-st-v1).CEL (18 total)
>  varLabels: sample
>  varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: hugene10stv1
>> write.exprs(eset_justrma,file="eset_justrma.csv")
>> write.exprs(eset_mas5,file="eset_mas5.csv")
>> write.exprs(eset,file="eset.csv")
>
> Any help in this will be really great. Being a novice, I am very  
> sorry if I
> am doing any silly mistake.
> Thanks a lot,
> Suparna.
>
> -- 
> Dr. Suparna Mitra
> Wolfson Centre for Personalised Medicine
> Department of Molecular and Clinical Pharmacology
> Institute of Translational Medicine University of Liverpool
> Block A: Waterhouse Buildings,  L69 3GL Liverpool
>
> Tel.  +44 (0)151 795 5414, Internal ext: 55414
> M: +44 (0) 7523228621
> Email id: smitra at liverpool.ac.uk
> Alternative Email id: suparna.mitra.sm at gmail.com
>
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>
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