Hello,
Can we use DESeq2 normalise count as input for pheatmap?
x<-counts(dds6Genus,normalized=TRUE)
heatmap(x,scale="row",color =colorRampPalette(c('blue','yellow'))(12),cluster_cols =F,show_colnames = T,cluster_row=T,border_color="NA", fontsize_row=10,fontsize =10)
Many thanks
One usually uses the normalized counts on the log scale, after Z transformation, see:
Is anything wrong in above command as we are taking normalize count and then in pheatmap we are doing scaling using "scale=row"?
Thank you so much, so should I used below set of commands?
x<-counts(dds6Genus,normalized=TRUE)
#For log transformation
x2 <- log2(x)
heatmap(x2,scale="row",color =colorRampPalette(c('blue','yellow'))(12),cluster_cols =F,show_colnames = T,cluster_row=T,border_color="NA", fontsize_row=10,fontsize =10)
Many thanks,
Sorry,Can we just do log transformation as updated in the code. Many thanks for your quick help.
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