[BioC] Analysis of Human Gene 1.1 ST Array

[James W. MacDonald]

Hi Jerry,

I am going to assume you saw and read the warning, considering you 
printed it out.

It says that you should be using the oligo or xps packages. So that is 
step #1. Use one of those two packages instead of the affy package.

There are vignettes for both packages that you can read to help you get 
started. Note that you can summarize the Gene ST arrays at either the 
transcript or probeset (roughly exon) level, so the annotation package 
you will need to map probesets to genes, etc, will either be the 
hugene11sttranscriptcluster.db or hugene11probeset.db package.

Best,

Jim



On Tuesday, November 05, 2013 5:49:56 PM, Jerry Cholo wrote:
> Hello,
>
>
>
> I need to analyze a microarray dataset that used Human Gene 1.1 ST Array.  When
> I ran following command lines:
>
>
>
> library(affy)
>
> library(limma)
>
> Data <- ReadAffy()
>
>
>
> I got this warning message and error:
>
>
>
> Warning message:
>
>
>
> The affy package can process data from the Gene ST 1.x series of arrays,
>
> but you should consider using either the oligo or xps packages, which are
> specifically
>
> designed for these arrays.
>
>
>
>> Data
>
> AffyBatch object
>
> size of arrays=1190x990 features (25 kb)
>
> cdf=HuGene-1_1-st-v1 (??? affyids)
>
> number of samples=20
>
> Error in (function (package, help, pos = 2, lib.loc = NULL, character.only
> = FALSE,  :
>
>    ‘hugene11stv1cdf’ is not a valid installed package
>
> In addition: Warning message:
>
> missing cdf environment! in show(AffyBatch)
>
>
>
> May someone let me know how I could fix this problem?
>
>
>
> Thanks,
>
> Jerry
>
> 	[[alternative HTML version deleted]]
>
>
>
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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