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Question: ExprSetbuilder Excel AddIn
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gravatar for Werre, Stephen
12.3 years ago by
Werre, Stephen10 wrote:
Dear R users, I am trying to import single channel cDNA microarray data into Bioconductor (Grant was written before recent advances). The challenges are two fold: 1) The exprSetbuilder Excel Addin has a small bug: Afunction in btnDataToR is called as Rinterface.REvalReturn but actually it should be called as RInterfaceSupport.REvalReturn. As a result, the program failed to run, and I failed to correct it!. 2) Looks like one can construct an exprSet object using Biobase (Vignette name = Textual Descriptoin of Biobase). However R has persistently told me that sample names in exprs are different from those in the phenoData object. Any help will be appreciated. Thanks, Stephen Werre
ADD COMMENTlink modified 12.3 years ago by Martin Morgan ♦♦ 22k • written 12.3 years ago by Werre, Stephen10
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gravatar for Martin Morgan
12.3 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
Hi Stephen -- I can help with the second part... > 2) Looks like one can construct an exprSet object using Biobase > (Vignette name = Textual Descriptoin of Biobase). However R has > persistently told me that sample names in exprs are different from those > in the phenoData object. The requirement is that the sample names in exprs (i.e., the colnames of the expression data matrix) match the row names of the phenoData. So following along in the vignette you mention: # This is the expression data, which is a matrix > data(geneData) > class(geneData) [1] "matrix" > colnames(geneData) [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" [20] "T" "U" "V" "W" "X" "Y" "Z" # .. and the 'pData' part of phenoData, which is a data.frame > data(geneCovariate) > class(geneCovariate) [1] "data.frame" > rownames(geneCovariate) [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" [20] "T" "U" "V" "W" "X" "Y" "Z" Your task is to ensure that this identity of column and row names is the case for your data, too. Hopefully this is done as far 'up-stream' as possible, e.g., in the files that you're reading in to R. Once in R it is of course also possible to assign row or column names to appropriate data components, e.g., > rownames(geneCovariate) <- letters[1:26] > rownames(geneCovariate) [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" [20] "t" "u" "v" "w" "x" "y" "z" (and if you were to try to create an exprSet now, you would end up with that pesky error about different sample names). Hope that's enough of a hint, Martin > Any help will be appreciated. > Thanks, > Stephen Werre > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 12.3 years ago by Martin Morgan ♦♦ 22k
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