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Old 04-29-2014, 07:57 AM   #1
Nico38
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Location: NL

Join Date: Nov 2013
Posts: 1
Default Gene ordered by ID using getGenes(), package CummeRbund

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
Rplot02.jpeg

The genes are ordered alphabetically and did not keep the order my list. Any thought?
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Old 07-07-2014, 10:45 AM   #2
millerma1
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Location: USA

Join Date: Jun 2014
Posts: 6
Default

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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csheatmap, cummerbund plots, getgenes(), heatmap

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