[BioC] Affystart function in Affycoretools

[Sachin Mathur]

Dear Users,

I have recently upgraded the bioconductor package to 2.0  from 1.9. The
affystart function in affycoretools used to work just fine with bioc 1.9
but I get the following errors on 2.0. 

>fnames = c("LKM1_051407.CEL","LKM2_051407.CEL")
> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
45101 ids to be processed
|                    |
|####################|
Getting probe level data...
Computing p-values
Making P/M/A Calls
Error in function (classes, fdef, mtable)  :
        unable to find an inherited method for function "se.exprs", for
signature "ExpressionSet"
In addition: Warning messages:
1: The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
2: Incompatible phenoData object. Created a new one.
 in: read.affybatch(filenames = filenames, phenoData = phenoData)
Execution halted


I tried to look for se.exprs, but couldn't make any headway. Here's the
output from sessionInfo()

> sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
"utils"
[7] "datasets"  "methods"   "base"

other attached packages:
    mouse4302  mouse4302cdf affycoretools       annaffy        xtable
     "1.16.0"      "1.16.0"       "1.8.0"       "1.8.1"       "1.4-6"
        gcrma   matchprobes       biomaRt         RCurl           XML
      "2.8.1"       "1.8.1"      "1.10.0"       "0.8-0"       "1.7-1"
        limma          affy        affyio       GOstats      Category
     "2.10.5"      "1.14.1"       "1.4.0"       "2.2.6"       "2.2.3"
       Matrix       lattice    genefilter      survival          KEGG
  "0.99875-2"      "0.15-4"      "1.14.1"        "2.31"      "1.16.1"
         RBGL      annotate       Biobase            GO         graph
     "1.12.0"      "1.14.1"      "1.14.0"      "1.16.0"      "1.14.2"

Thanks for the help,

Sachin Mathur
2027 Kansas Life Sciences Innovations Center
3901 Rainbow Blvd. 
Kansas City, KS 66160-7401 
Phone: (913) 588-5966 
Fax: (913) 588-5677 
smathur at kumc.edu