Question: Error in `rownames<-`(`*tmp*`, value = list(genes
gravatar for mictadlo
8 months ago by
mictadlo0 wrote:

Hi, I folled this instructions but I got the bellow error:

> logCPM <- cpm(y, prior.count=2, log=TRUE)
> head(y$genes)
3  sp0025247
4  sp0025250
5  sp0025268
6  sp0025270
8  sp0025282
12 sp0056834
> y$samples$group
 [1] Root_tip.1.5 Root_tip.1.5 Root_tip.1.5 Root_tip.1.5 Leaves.1.5   Leaves.1.5  
 [7] Leaves.1.5   Leaves.1.5   Root_tip.2   Root_tip.2   Root_tip.2   Root_tip.2  
[13] Leaves.2     Leaves.2     Leaves.2     Leaves.2     Root_tip.3   Root_tip.3  
[19] Root_tip.3   Root_tip.3   Leaves.3     Leaves.3     Leaves.3     Leaves.3    
Levels: Leaves.1.5 Leaves.2 Leaves.3 Root_tip.1.5 Root_tip.2 Root_tip.3
> rownames(logCPM) <- y$genes
Error in `rownames<-`(`*tmp*`, value = list(genes = c("sp0025247", "sp0025250",  : 
  length of 'dimnames' [1] not equal to array extent
> dim(y$genes)
[1] 58971     1
> dim(rownames(logCPM))
> dim(logCPM)
[1] 58971    24

What did I miss?

Thank you in advance

ADD COMMENTlink modified 8 months ago by Aaron Lun19k • written 8 months ago by mictadlo0
gravatar for Aaron Lun
8 months ago by
Aaron Lun19k
Cambridge, United Kingdom
Aaron Lun19k wrote:

As y$genes is a data.frame, you obviously can't use it as the row names. You need the character vector of gene names instead, i.e., y$genes$genes.

ADD COMMENTlink written 8 months ago by Aaron Lun19k
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