[BioC] ExprSetbuilder Excel AddIn

[Martin Morgan]

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
>
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