Question: Error in, num.rows, num.cols, mat, as.integer(num.figures)
gravatar for mictadlo
7 weeks ago by
mictadlo0 wrote:

Hi, I have followed this paper but for my data I got the below error:

> logCPM <- cpm(y, prior.count=2, log=TRUE)
> head(y$genes$genes)
[1] "sp0025247" "sp0025250" "sp0025268" "sp0025270" "sp0025282" "sp0056834"
> y$samples$group
 [1] Root_tip.1.5 Root_tip.1.5 Root_tip.1.5 Root_tip.1.5 Leaves.1.5   Leaves.1.5   Leaves.1.5   Leaves.1.5   Root_tip.2  
[10] Root_tip.2   Root_tip.2   Root_tip.2   Leaves.2     Leaves.2     Leaves.2     Leaves.2     Root_tip.3   Root_tip.3  
[19] Root_tip.3   Root_tip.3   Leaves.3     Leaves.3     Leaves.3     Leaves.3    
Levels: Leaves.1.5 Leaves.2 Leaves.3 Root_tip.1.5 Root_tip.2 Root_tip.3
> rownames(logCPM) <- y$genes$genes
> colnames(logCPM) <- paste(y$samples$group, 1:2, sep="-")
> o <- order(tr$table$PValue)
> logCPM <- logCPM[o[1:30],]
> logCPM <- t(scale(t(logCPM)))
> library(gplots)
> col.pan <- colorpanel(100, "blue", "white", "red")
> heatmap.2(logCPM, col=col.pan, Rowv=TRUE, scale="none",
+           trace="none", dendrogram="both", cexRow=1, cexCol=1.4,"none",
+           magin=c(10,9), lhei=c(2,10), lwid=c(2,6))
Error in, num.rows, num.cols, mat, as.integer(num.figures),  : 
  invalid graphics state

What did I miss?

Thank you in advance.

ADD COMMENTlink modified 6 weeks ago by Aaron Lun17k • written 7 weeks ago by mictadlo0
gravatar for Aaron Lun
6 weeks ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

It's easy to help yourself. A bit of Googling brings up posts like:

... which suggest running before attempting to make the plot.

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Aaron Lun17k
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