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-   -   Gene ordered by ID using getGenes(), package CummeRbund (http://seqanswers.com/forums/showthread.php?t=42912)

Nico38 04-29-2014 06:57 AM

Gene ordered by ID using getGenes(), package CummeRbund
 
1 Attachment(s)
I want to produce a heat-map using a costumed gene list (accession IDs, e.g AT1G73590). I made a list of genes ordered depending on the processes they are involve in. I would like to conserve this order when I am plotting the expression value in csHeatmap(), but they end up ordered alphabetically.

Code:

Cand_GenesIds= as.character(Gene_name_ID[,3])
head(Cand_GenesIds)
[1] "AT1G19850" "AT1G73590" "AT4G32880" "AT5G16560" "AT1G32240" "AT4G17695"

Then I recover the FPKM from cuffdiff using getGenes

Code:

Can_Genes<-getGenes(cuff, Cand_GenesIds)
I plot the expression data using csHeatmap()

Code:

can.rep<-csHeatmap(Can_Genes,cluster="none",replicates=F, fullnames=F)
can.rep

Attachment 3010

The genes are ordered alphabetically and did not keep the order my list. Any thought?

millerma1 07-07-2014 09:45 AM

I am having the same exact problem. Trying to view ~100 genes in a specific order. Anyone have any idea how to do this?


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