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caiwei@mdanderson.org
▴
110
@caiweimdandersonorg-1599
Last seen 10.3 years ago
Dear all,
I am running RMA and MAS5 on some U133_Pluss_2 array and get this
warning
message :
> x.rma <- as(rma(ab), "ExpressionSet")
Warning messages:
1: missing or mis-shaped 'se.exprs' in original object; creating
ExpressionSet without se.exprs in: asMethod(object)
2: contents of varLabels ignored
> x.mas <- as(x.mas, "ExpressionSet")
Warning messages:
1: missing or mis-shaped 'se.exprs' in original object; creating
ExpressionSet without se.exprs in: asMethod(object)
2: contents of varLabels ignored
I used these code lines:
fnames <- paste(as.character(pData(pd)$ArrayName), "CEL", sep=".")
ab <- read.affybatch(filenames=fnames, phenoData=pd,
description=miame)
x.mas <- as(x.mas, "ExpressionSet")
x.rma <- as(rma(ab), "ExpressionSet")
Background correcting
Normalizing
Calculating Expression
R version 2.4.1 (2006-12-18)
i686-pc-linux-gnu
other attached packages:
hgu133plus2cdf ClassDiscovery cluster ClassComparison
PreProcess
"1.14.0" "1.3" "1.11.4" "1.3"
"1.3"
oompaBase xtable colorspace geneplotter
annotate
"1.3" "1.4-3" "0.95" "1.12.0"
"1.12.1"
simpleaffy genefilter survival affy
affyio
"2.4.2" "1.12.0" "2.30" "1.12.2"
"1.2.0"
Biobase
"1.12.2"
Highly appreciate any comments!
Caimiao Wei
UT M.D.Anderson Cancer Center
1515 Holcombe Blvd, Unit 237
Houston, TX 77030-4009