cummeRbund andplotting for selected treatments among multiple treatments

ataheri · 03-22-2013, 11:31 AM

I have 16 different treatments which are t-tested in cuffdiff and I was wondering if there is a way to plot (like expressionBarplot) in cummeRbund for some of these treatments and not all of them.
in sVolcano we can tell the output to be for just two samples like this:

csVolcano(genes(cuff),'hESC', 'Fibroblasts')

but for expressionBarplot we dont have this option.

lgoff · 04-10-2013, 07:41 PM

Check out the 'sampleIdList' argument to getGenes(). This should do what you require.

Cheers,
Loyal

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03-22-2013, 11:31 AM	#1
ataheri Junior Member Location: Nashville, TN Join Date: Nov 2011 Posts: 7	cummeRbund andplotting for selected treatments among multiple treatments I have 16 different treatments which are t-tested in cuffdiff and I was wondering if there is a way to plot (like expressionBarplot) in cummeRbund for some of these treatments and not all of them. in sVolcano we can tell the output to be for just two samples like this: csVolcano(genes(cuff),'hESC', 'Fibroblasts') but for expressionBarplot we dont have this option.

04-10-2013, 07:41 PM	#2
lgoff Member Location: Cambridge, MA Join Date: Feb 2008 Posts: 82	Check out the 'sampleIdList' argument to getGenes(). This should do what you require. Cheers, Loyal