Usually by the time I get to cummeRbund (having run TopHat, cufflinks, cuffmerge and cuffdiff) I see something in the dispersionPlot that looks at least vaguely diagonal, and in the csDensity plot that looks at least semi-normal.
I've just done a study comparing cells exposed to media only and to media + a chemical compound. The idea is to look for genes that are differentially expressed when exposed to the chemical compound.
There were 3 replicates for each (control and treatment).
I've run TopHat with the gtf file for hg19 (these are human cells), then cufflinks, cuffmerge, cuffdiff (in mostly the standard ways) and got plots that look like nothing I've seen before.
I re-rand cuffdiff with an upper-diagnol normalization, but honestly if these plots show fpkm I don't think that would have changed anything.
My csScatter is pretty well centered on the diagonal, so I think normalization worked well. csBoxplots, with and without replicates, also look like what I usually see, though the IQRs are a little longer than usual.
So what might be going on here, and should I be worried about my results?
What's causing that "tail" in the dispersion plot?
Any advice or insights would be greatly appreciated!
Hopefully these attached images work:
I've just done a study comparing cells exposed to media only and to media + a chemical compound. The idea is to look for genes that are differentially expressed when exposed to the chemical compound.
There were 3 replicates for each (control and treatment).
I've run TopHat with the gtf file for hg19 (these are human cells), then cufflinks, cuffmerge, cuffdiff (in mostly the standard ways) and got plots that look like nothing I've seen before.
I re-rand cuffdiff with an upper-diagnol normalization, but honestly if these plots show fpkm I don't think that would have changed anything.
My csScatter is pretty well centered on the diagonal, so I think normalization worked well. csBoxplots, with and without replicates, also look like what I usually see, though the IQRs are a little longer than usual.
So what might be going on here, and should I be worried about my results?
What's causing that "tail" in the dispersion plot?
Any advice or insights would be greatly appreciated!
Hopefully these attached images work:
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