[BioC] SimpleAffy: problem with Yeast Genome 2.0 Array

[Crispin Miller]

Hi Earl,
This is because the package needs some information about each array type
to work out QC parameters (e.g. 3'/5' ratios, etc.) The yeast genome 2.0
array is currently not represented in the package - I'll add it and let
you know.


Crispin


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Earl F.
Glynn
Sent: 08 November 2005 20:14
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] SimpleAffy: problem with Yeast Genome 2.0 Array

I'm trying to use SimpleAffy with four Yeast Genome 2.0 Array GeneChips.

When I ran my R script the first time, the needed cdf file seemed to be
installed automatically:

Background correcting
trying URL
'http://bioconductor.org/packages/data/annotation/1.7/bin/windows/contri
b/2.
2/yeast2cdf_1.10.0.zip'
Content type 'application/zip' length 832343 bytes opened URL downloaded
812Kb

package 'yeast2cdf' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Documents and Settings\efg\Local
Settings\Temp\Rtmp1643\downloaded_packages
updating HTML package descriptions
Retrieving data from AffyBatch...done.
Computing expression calls...
....done.
scaling to a TGT of 100 ...
Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale
factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor
for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for:
B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825 Error in
qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip
type: yeast2cdf


Now when I run the lines from my script manually, I seem to be stuck
getting the "qc" command to recognize the Yeast Genome 2.0 Array:

>  x <- read.affy("SimpleAffy.txt",path=CELpath)
>  x.mas5 <- call.exprs(x, "mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
....done.
scaling to a TGT of 100 ...
Scale factor for: A_pot1-_mRNA_Yeast_2.CEL 0.060815902286448 Scale
factor for: A_pot1-_totalRNA_Yeast_2.CEL 0.0588578984707041 Scale factor
for: B_wt_mRNA_Yeast_2.CEL 0.0591585374701625 Scale factor for:
B_wt_totalRNA_Yeast_2.CEL 0.0705377276149825
>  x.qc   <- qc(x, x.mas5)
Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
chip
type: yeast2cdf

Can anyone suggest what I should do to get around this problem?

Thanks in advance for any help.

efg
--
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research

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