[BioC] RMA warning message about missing se.exprs

[caiwei at mdanderson.org]

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