Hello,
In working with HTqPCR lately I noticed that the gene/feature names are not produced in the output of limmaCtData, even if they are present in the input. This isn't an issue with ttestCtData. Before I realized that there was an option for not sorting the results by p-value, I was a little puzzled by how I would annotate multiple comparisons, so it would definitely be helpful if the gene names appeared in the output. Unless I'm doing something wrong, but that doesn't seem to be the case. Sorry I didn't check the code for this myself yet to see if it's something I can add.

I also noticed in the vignette (p34 in the most recent BioC release) that limmaCtData is run with default sort option, which would sort by p-value. These results are then fed into the heatmapSig method, which appears to combine the ddCt values from the multiple comparisons in whatever order the rows might be in for each comparison. This is fine if limmaCtData if sort=FALSE is used, since the rows for all the comparisons will be in the same order. When the results are sorted, the combined matrix that's used for the heatmapSig heatmap might actually have a different row order for each column. It would be good if that was clearer in the vignette.

Thanks!

Adam Cornwell
Programmer/Analyst
Center for Translational Neuromedicine

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