[BioC] Estrogen data error in genelist

[Keith Satterley]

Hi Thomas,

There is an updated approach to the Estrogen example analysis. It is at
http://bioinf.wehi.edu.au/marray/bioc2005/estrogen.html
which doesn't have the problems of the ibc2004/lab3 example.
We have checked it out this afternoon and it works correctly,

Keith Satterley
Bioinformatics  Division
The Walter and Eliza Hall Institute of Medical Research

Thomas Curtis wrote:

>*Hi All,*
>**
>*I tried to do a run through with the estrogen dataset as described in Lab3:
>**http://bioinf.wehi.edu.au/marray/ibc2004/lab3/lab3.html*<http://bioinf.wehi.edu.au/marray/ibc2004/lab3/lab3.html>
>*but encounted an error when trying to hyperlink the topTable list to
>Unigene and GenBank info.*
>**
>*Following the the code provided in the lab:*
> library(hgu95av2cdf)
>library(hgu95av2)
>geneIDs <- ls(hgu95av2cdf)
>geneSymbols <- unlist(as.list(hgu95av2SYMBOL))
>geneNames <- unlist(as.list(hgu95av2GENENAME))
>geneNames <- substring(geneNames,1,40)
>unigene <- unlist(as.list(hgu95av2UNIGENE))
>unigene <- gsub("Hs\\.","",unigene)
>  genelist <- data.frame(GeneID=geneIDs,GeneSymbol=geneSymbols,GeneName=geneNames,
>UniGeneHsID=paste("<a href=
>http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=",
>unigene,">",unigene,"</a>",sep=""))
> *I get the following error:*
>  Error in data.frame(GeneID = geneIDs, GeneSymbol = geneSymbols, GeneName =
>geneNames, :
>arguments imply differing number of rows: 12625, 12744
> *How can I rectify this problem so that the number of entries is the same?*
>**
>*Many Thanks,*
>*Tom*
>
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