Dear Richard,
 Thank you very much for the quick response.
Being new in this area I was bit confused with the options. Can you suggest
any quick tutorial which can help be in self learning these options?
hanks a lot,
Suparna.

On 11 June 2012 16:03, Richard Friedman
<friedman@cancercenter.columbia.edu>wrote:

> 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@cancercenter.**columbia.edu <friedman@cancercenter.columbia.edu>
> http://cancercenter.columbia.**edu/~friedman/<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@liverpool.ac.uk
>> Alternative Email id: suparna.mitra.sm@gmail.com
>>
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>>
>
>


-- 
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@liverpool.ac.uk
Alternative Email id: suparna.mitra.sm@gmail.com

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