[BioC] simpleaffy and yeast2cdf problems

[Alvord, Greg (DMS) [Contr]]

Hi Dan - 

This is the post I sent out only last week that may assist you with your
problem. 

https://stat.ethz.ch/pipermail/bioconductor/2007-January/015514.html

We ran into a similar problem with the soybeancdf environment.  
Hope this helps.  

	Greg 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dan Swan
Sent: Monday, January 08, 2007 6:49 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] simpleaffy and yeast2cdf problems

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
Tel: +44 (0)191 222 7253 (Leech: Rooms M.2046/M.2046A - Mon/Wed)
Tel: +44 (0)191 246 4833 (Devonshire: Rooms G.25/G.26 - Thu/Fri)
Website: http://bsu.ncl.ac.uk/

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