Replicates in ExpressionSet

Question

[jacobsen.jeremy]

I'm trying to benchmark TDAracne for gene network reconstruction on a simulated dataset. TDAracne takes in data as an ExpressionSet. This is my first time dealing with ExpressionSets or anything meant for microarray data. I have been able to construct an ExpressionSet object from scratch using the Bioconductor explanation here:

https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf

The problem is that I have replicate data and don't know how to build an ExpressionSet with replicates. This does not seem to be mentioned in the ExpressionSet or TDAracne documentation. Does anyone have any guidance?

Thanks,

-Jeremy

Answer 1

[Ahill]

There should be no problem with creating an ExpressionSet including replicate samples, using the instructions you linked. Are you getting a specific error message? You would want each column of the expression matrix to have a unique name, and then you can use the phenoData object to indicate which samples are replicates. For example, if you had 3 replicates of sample A, your expression matrix column names could be be A-1, A-2, A-3, and in the phenoData you would define a factor where all 3 replicates were labeled 'A' to indicate they are replicates.