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Old 04-29-2012, 04:38 PM   #2
Junior Member
Location: Eastern US

Join Date: Apr 2012
Posts: 3


I would start by checking that the ExonContSet (ecs) was built correctly.

A couple of things to try

design(ecs) - This should match what you intended.

sampleNames(ecs) - the row names of the design output should match this

table(geneIDs(ecs)) will show you how many genes are in the set.

you can also try head(modelFrameforGene(ecs, "Pick some gene" )) of course replace the Pick some gene with the name of a gene from your genome.
This will show if something for counts was read in.

Also normally the values for replicate would be 1,2, and 3 for each sample type. I don't think having them all set to one will cause a problem, but I have never tried it.

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