How to build a heatmap using cummerbund with user defined list of genes

[psingh]

Hi
I am a newbie learning to use cummerbund for analyzing RNA Seq data.
I need to build some heatmaps with a list of genes across 2 samples.
My code is:

common=c("PLK1","MYBL2","CCND1","CCNB1","E2F1","FOXM1","TOP2A")
> testcommon=getGenes(cuff1,common)
>csHeatmap(testcommon,rescaling='none',clustering='none',labCol=F,labRow=T,logMode=T,pseudocount=1.0,border=FALSE,heatscale=c(low='green',mid='black',high='red'),heatMidpoint=NULL)
The heatmap is attached
However the order of the genes is random and changes each time my samples change. Could somebody please help me order the genes the way I want?

Thanks

[jp.]

Hi
Did you get answer ?
You may try using clustering='both'.
Do you something about error bars in expressionBarplot(mygene), I have very high (big) error bars ??? is it a big error or just can be ignored ?

[jp.]

Hi
do you know, if we can add a dendrogram using csHeatmap ?
Thank you

Hi
I am a newbie learning to use cummerbund for analyzing RNA Seq data.
I need to build some heatmaps with a list of genes across 2 samples.
My code is:

common=c("PLK1","MYBL2","CCND1","CCNB1","E2F1","FOXM1","TOP2A")
> testcommon=getGenes(cuff1,common)
>csHeatmap(testcommon,rescaling='none',clustering='none',labCol=F,labRow=T,logMode=T,pseudocount=1.0,border=FALSE,heatscale=c(low='green',mid='black',high='red'),heatMidpoint=NULL)
The heatmap is attached
However the order of the genes is random and changes each time my samples change. Could somebody please help me order the genes the way I want?

Thanks

[shleshar]

Hi psingh,

Did you manage to find a way to order the genes? Cannot find how to?

Thanks

[jp.]

I shifted to gplots.
cummeRbund gives lot scale and without normalization, it is not accepted for publication. I dont know how to normalise using R. Therefore, I mannualy normalized values and created heatmap.

Hi psingh,

Did you manage to find a way to order the genes? Cannot find how to?

Thanks