Dear Jim,
  Thanks a lot. Yes I also read something that  HuGene array does not use
the T7-Oligo(dT) primer. But sorry being new I just missed the point.
Actually I was trying to follow a step by step tutorial for Affy data.

But can you suggest the best way to perform qc for this chip?
Thanks a lot,
Suparna.

On 4 September 2012 16:58, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Suparna,
>
>
> On 9/4/2012 11:35 AM, suparna mitra wrote:
>
>> Hello group,
>>   I am new in bioconductor and trying use it for my Affymetrix microarray
>> data.
>> Genechip HuGene-1_0-st-v1.
>>
>
> The simpleaffy package isn't really designed for this array. A significant
> portion of the QC measures are based on comparisons between the PM and MM
> probes, and the newer generation of arrays from Affy no longer have MM
> probes.
>
> Best,
>
> Jim
>
>
>
>> I have normalized my data using rma. Then when I trying to see the quality
>> I found following error. Can anybody help me with this please.
>> Thanks a lot in advance :)
>> Best wishes,
>> Suparna.
>>
>>  library(affy)
>>> library(simpleaffy)
>>>
>> Loading required package: genefilter
>> Loading required package: gcrma
>>
>> Attaching package: 'simpleaffy'
>>
>> The following object(s) are masked _by_ '.GlobalEnv':
>>
>>      getBioC
>>
>>  library("hugene10stv1cdf")
>>> aqc<-qc(InVivodata)
>>>
>> Error in setQCEnvironment(cdfn) :
>>    Could not find array definition file ' hugene10stv1cdf.qcdef '.
>> Simpleaffy does not know the QC parameters for this array type.
>> See the package vignette for details about how to specify QC parameters
>> manually.
>>
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>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>


-- 
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 5394, Internal ext: 55394
M: +44 (0) 7511387895
Email id: smitra@liverpool.ac.uk
Alternative Email id: suparna.mitra.sm@gmail.com

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