Question: CummeRbund heatmap not showing all listed genes
0
gravatar for V
2.9 years ago by
V110
UK/London
V110 wrote:

Hello,

Im running CummRbund on R but having a weird issue when generating heatmaps. I load in my files, all the functions seem to be working fine (dispersion plot, volcano plot etc), but when I input a list of genes using the following command:

myGenesId <- c("NM_021279","NM_001256224", "NM_023653","NM_009520","NM_009521", "NM_009522")
myGenes<-getGenes(cuff,myGenesId)
h<-csHeatmap(myGenes)
h

CummRbund generates a heatmap but some/most of the genes listed are missing. I've gone back to the original tabular file to check if all of those genes are there and they are with quite high FPKM values so not sure why it just omits some of them.

Any help would be really appreciated. Thanks

cummerbund • 915 views
ADD COMMENTlink written 2.9 years ago by V110

Did you check if you have all the genes in the myGenes object? In case, can you upload your dataset?

ADD REPLYlink written 2.9 years ago by Selenocysteine550

Yes, looking at the myGenes object lists all 18 of the variables i've added but the heatmap only generates 5 of them.

ADD REPLYlink written 2.9 years ago by V110
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