[BioC] Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: moe430acdf

[Crispin Miller]

Hi Dick,
I believe the problem is fixed in the version of simpleaffy in the Devl
branch (2.07). I'll also update the release version - in the meantime
try the version from the devl release. 

Cheers,
Crispin
 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dick Beyer
Sent: 19 January 2005 00:03
To: Bioconductor
Subject: [BioC] Error in qc.affy(unnormalised, ...) : I'm sorry, I do
not know about chip type: moe430acdf

I am getting an error when I try the simpleaffy routine qc() on a set of
moe430a chips.

exp1.all.raw <- ReadAffy(widget=T)
exp1.all.raw
AffyBatch object
size of arrays=712x712 features (51493 kb) cdf=MOE430A (22690 affyids)
number of samples=13 number of genes=22690 annotation=moe430a

exp1.mas5 <- call.exprs(exp1.all.raw,"mas5")
qc        <- qc(exp1.all.raw,exp1.mas5)
Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
chip type: moe430acdf

qc.affy calls haveQCParams, but haveQCParams shows:
> rownames(get("alpha", envir = .qcEnv))
  [1] "atgenomecdf"    "ath1121501cdf"  "drosgenome1cdf" "hcg110cdf"
"hgfocuscdf"
  [6] "hgu133acdf"     "hgu133a2cdf"    "hgu133atagcdf"  "hgu133bcdf"
"hgu133plus2cdf"
[11] "hgu95acdf"      "hgu95av2cdf"    "hgu95bcdf"      "hgu95ccdf"
"hgu95dcdf"     
[16] "hgu95ecdf"      "mgu74acdf"      "mgu74av2cdf"    "mgu74bcdf"
"mgu74bv2cdf"   
[21] "mgu74ccdf"      "mgu74cv2cdf"    "mouse4302cdf"   "mouse430acdf"
"mouse430a2cdf" 
[26] "mouse430b2cdf"  "mu11ksubacdf"   "mu11ksubbcdf"   "rae230acdf"
"rae230bcdf"    
[31] "rgu34acdf"      "rgu34bcdf"      "rgu34ccdf"      "ygs98cdf"
"zebrafishcdf"  
[36] "rat2302cdf"

so qc() is expecting mouse430a, instead, it gets moe430a.

I remember some discussion of this issue some time ago, but was unable
to find it in the mail archives.

My windows packages are:
base 2.0.1
datasets 2.0.1
utils 2.0.1
grDevices 2.0.1
graphics 2.0.1
stats 2.0.1
methods 2.0.1
tools 2.0.1
Biobase 1.5.0
reposTools 1.5.1
affy 1.5.8
matchprobes 1.0.12
gcrma 1.1.1
qvalue 1.1
siggenes 1.2.11
limma 1.8.6
GO 1.6.4
KEGG 1.6.2
annotate 1.5.1
annaffy 1.0.11
moe430a 1.6.8
moe430acdf 1.4.3
moe430aprobe 1.0
simpleaffy 2.01
tcltk 2.0.1
widgetTools 1.4.7
DynDoc 1.5.0
tkWidgets 1.5.20
xtable 1.2-4

Thanks very much for any help or suggestions.

Thanks,
Dick
************************************************************************
*******
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html

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