[BioC] SimpleAffy: problem with Yeast Genome 2.0 Array

[Jenny Drnevich]

Hi Crispin,

I've run into similar errors with a variety of different chip types, e.g. 
E.coli2, "remapped" CDFs for human-mouse-rat (available at 
http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp 
). Is there any way for the end user to modify this so I don't have to bug 
you every time I want to try out an unusual CDF? I looked at the code, and 
all the needed info about spike-in probes and qc.probes are stored in 
the  .qcEnv. If I knew what format this data needed to be in, I could 
create it and then change the code to look for it elsewhere.

Thanks,
Jenny

At 07:09 AM 11/10/2005, Crispin Miller wrote:
>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
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>--------------------------------------------------------
>
>
>This email is confidential and intended solely for the use o...{{dropped}}
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu