Entering edit mode
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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Hi there,
Exactly the same problem here. It would be really nice if HTqPCR maintainers fix this. From the vignette looks like the ttestCtData and mannwhitneyCtData functions output feature names, however they don't at least for HTqPCR_1.22.0