[BioC] Affy High Throughput arrays

[James W. MacDonald]

Hi Sanchita,

sanchita at MIT.EDU wrote:
> 
> Hi,
> 
> I am trying to normalize 64 High Throughput Affy Human arrays in Bioconductor
> using GCRMA package.
> 
> One of the hurdles in running justgcrma() is under MetaData section on
> Bioconductor site I didn't find the HT_Hgu133A cdf and probe files. Does
> anybody has any clue.
> 
> I  was able to download the HT_Hgu133A cdf file from the Affy Netaffx site but
> don't know how to make a package out of it that would run on Bioconductor.

I don't see this file. Can you give me a link?

My understanding was that the 133A HT plate simply had 96 133A_v2 chips, 
so I assumed that you got 96 celfiles when you read the plate, and could 
use the regular 133av2cdf package. Do you not get 96 celfiles?

Best,

Jim


> 
> Any help on this matter will be highly apprecaited.
> 
> 
> Thanks,
> 
> Sanchita
> 
> P.S. Error message as follows:
> 
> 
>>normalized<-justGCRMA()
> 
> Computing affinities[1] "Checking to see if your internet connection works..."
> [1] "Environment hthgu133acdf was not found in the Bioconductor repository."
> [1] "Checking to see if your internet connection works..."
> [1] "Environment hthgu133aprobe was not found in the Bioconductor repository."
> Error in get(x, envir, mode, inherits) : variable "hthgu133aprobe" was not found
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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