[BioC] simpleaffy and yeast2cdf problems

[Jenny Drnevich]

Hi Dan,

See the very recent post by Greg Alford:
https://stat.ethz.ch/pipermail/bioconductor/2007-January/015514.html

They have modified the code of qc() so that it will work for unknown chip 
types. Although he is calling his code soybean.mod.qc.affy(), there is 
nothing specific for the soybean array so it can be used for any chip type. 
However, it doesn't give all the information that qc() does; the spike-in 
probes, other qc probes and bioB hyb controls are specific for each chip 
and had to be left out. If you know these for your chip type, you might be 
able to modify the original code (commented out in soybean.mod.qc.affy) to 
include them.

Cheers,
Jenny

At 05:49 AM 1/8/2007, Dan Swan wrote:
>Hi Bioconductorites,
>
>I've seen references to this problem in 2005
>(https://stat.ethz.ch/pipermail/bioconductor/2005-November/010865.html)
>and 2006 (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012480.html),
>the former suggesting it should be fixed, but I'm still having the
>same issue.
>
>I just want some quick and dirty QC measures on some chips I am pretty
>sure are duff.
>
>following along with the outline in the "QC and Affymetrix data" pdf:
>
> > ampli.data<-read.affy("phenodata")
> > ampli.eset<-call.exprs(ampli.data,"mas5")
>Background correcting
>Retrieving data from AffyBatch...done.
>Computing expression calls...
>..............................done.
>scaling to a TGT of 100 ...
>Scale factor for: Yeast0wt1.CEL 0.1877573661054
>Scale factor for: Yeast0wt2.CEL 0.169107349891647
>Scale factor for: Yeast0wt3.CEL 0.176890842235261
>Scale factor for: Yeast1wt1.CEL 0.114515875199183
>Scale factor for: Yeast1wt2.CEL 0.132867931840117
>Scale factor for: Yeast1wt3.CEL 0.201211860669323
>Scale factor for: Yeast2wt1.CEL 0.120553407334518
>Scale factor for: Yeast2wt2.CEL 0.110981821370179
>Scale factor for: Yeast2wt3.CEL 0.12635084302873
>Scale factor for: Yeast3wt1.CEL 0.133156738139789
>Scale factor for: Yeast3wt2.CEL 0.119446187371786
>Scale factor for: Yeast3wt3.CEL 0.136591273338234
>Scale factor for: Yeast4wt1.CEL 0.143174910484902
>Scale factor for: Yeast4wt2.CEL 0.127534874666620
>Scale factor for: Yeast4wt3.CEL 0.177048335355844
>Scale factor for: Yeast0mut1.CEL 0.126568563373901
>Scale factor for: Yeast0mut2.CEL 0.177828594244113
>Scale factor for: Yeast0mut3.CEL 0.113037148372224
>Scale factor for: Yeast1mut1.CEL 0.125912932405511
>Scale factor for: Yeast1mut2.CEL 0.167309068269027
>Scale factor for: Yeast1mut3.CEL 0.134897445983855
>Scale factor for: Yeast2mut1.CEL 0.136284006808245
>Scale factor for: Yeast2mut2.CEL 0.197169068283275
>Scale factor for: Yeast2mut3.CEL 0.149844757694802
>Scale factor for: Yeast3mut1.CEL 0.119095781239726
>Scale factor for: Yeast3mut2.CEL 0.155941398564195
>Scale factor for: Yeast3mut3.CEL 0.144702217239922
>Scale factor for: Yeast4mut1.CEL 0.183634382620250
>Scale factor for: Yeast4mut2.CEL 0.180182357563251
>Scale factor for: Yeast4mut3.CEL 0.152303319246271
> > qc.data<-qc(ampli.data, ampli.eset)
>Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
>chip type: yeast2cdf
>
>which is the same error that has been reported before.
>
>sessionInfo() follows:
>
> > sessionInfo()
>R version 2.4.1 (2006-12-18)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
>Kingdom.1252;LC_MONETARY=English_United
>Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
>attached base packages:
>[1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
>"utils"     "datasets"
>[8] "methods"   "base"
>
>other attached packages:
>  yeast2cdf simpleaffy genefilter   survival       affy     affyio    Biobase
>   "1.14.0"    "2.8.0"   "1.12.0"     "2.30"   "1.12.2"    "1.2.0"   "1.12.2"
>
>any help would be appreciated.
>
>regards,
>
>Dan
>
>--
>Research Support Officer, Bioinformatics Support Unit,
>Institute for Cell and Molecular Biosciences,
>Faculty of Medical Sciences, Framlington Place,
>University of Newcastle upon Tyne, Newcastle, NE2 4HH
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>
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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
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ph: 217-244-7355
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e-mail: drnevich at uiuc.edu