[BioC] Trying to create exprSet

[Martin Morgan]

Hi Sally -- have a look at the vignette 'An introduction to Biobase and
ExpressionSets', section 4.1, if you haven't already.

> library(Biobase)
> openVignette()

The vignette is also available as 'ExpressionSetIntroduction.pdf' at

http://bioconductor.org/packages/2.1/bioc/html/Biobase.html

>From what you've written, myexprdata needs to be a matrix, perhaps

> myexprdata <- as.matrix(myexprdata)

will work. If phenotypicdata is a data.frame with the correct
information, then the next step should be

> adf <- new("AnnotatedDataFrame", data=phenotypicdata)
> eset <- new("ExpressionSet", exprs=myexprdata, phenoData=adf)

The vignette goes through additional details. There are example files
in Biobase that the vignette points you to if you need some more
help. If you run in to problems, you'll need to provide a bit more
information, especially the error message(s) that you encounter.

Toward the end of the vignette, in section 4.5, there's a 'minimal'
expression set, with just

> new("ExpressionSet", exprs=myexprdata)

and that might be a good place to start if you're frustrated.

Please also include the output of

> sessionInfo()

so that others can see what version of R and Biobase you're using --
hopefully you're using a recent version of R (2.6.0 or 2.6.1) and
you've either used biocLite to install Biobase, and / or the
instructions at

http://www.bioconductor.org/download

for information on updating packages.

Hope that helps,

Martin

Sally <sagoldes at shaw.ca> writes:

> I have read in my data with the following:
>
> myexprdata<-read.table("exprMatrix.txt", header=TRUE) 
> phenotypicdata<-read.table("phenotypicdata.txt",header=TRUE) 
>
> but despite working on it all day I haven't yet been able to create an exprSet.  Could someone help me?  Please!!!
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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