[BioC] Affystart function in Affycoretools

[Sachin Mathur]

Dear Jim,

I finally managed to get our IT to sort out the firewall issue and
update the packages as you had indicated, but I still get the same
error.

> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
31099 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

> 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:
   rat2302cdf affycoretools       annaffy        xtable         gcrma
     "1.16.0"       "1.8.0"       "1.8.1"       "1.4-6"       "2.8.1"
  matchprobes       biomaRt         RCurl           XML       GOstats
      "1.8.1"      "1.10.1"       "0.8-0"       "1.7-1"       "2.2.6"
     Category        Matrix       lattice    genefilter      survival
      "2.2.3"  "0.999375-0"      "0.16-2"      "1.14.1"        "2.32"
         KEGG          RBGL      annotate            GO         graph
     "1.16.1"      "1.12.0"      "1.14.1"      "1.16.0"      "1.14.2"
        limma          affy        affyio       Biobase
     "2.10.5"      "1.14.2"       "1.4.1"      "1.14.1"

While updating the packages, I got some warnings w.r.t. the Matrix
package, but did not get any error messages.

Regards,
Sachin


>>> "James W. MacDonald" <jmacdon at med.umich.edu> 7/5/2007 4:14 PM >>>
Hi Sachin,

Sachin Mathur wrote:
> 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"

Looks like mismatched versions. Both affy and affycoretools are old. I

would update:

biocLite("Biobase")
library(Biobase)
repos <- biocReposList()
update.packages(repos=repos, ask=FALSE)

Best,

Jim


> 
> 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 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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