gravatar for Aynur

2 hours ago by

I am doing differential gene expression analysis using DESeq2. I want to make an expression heat map of sample-to-sample distances on the matrix of variance-stabilized data(rlog).
I followed this code.

rld <- rlog(Merged_dds, blind=TRUE)
rld_mat <- assay(rld)
rld_cor <- cor(rld_mat)
pheatmap(rld_cor, annotation = select(Merged_metadata, condition))
heat.colors <- brewer.pal(6, "Blues")

I got a heatmap for all samples(10 samples, with 4 different treatments, and one control). Each condition has 2 biological replicates. But I want to make a similar heatmap for only one condition vs control. I have 2 replicates for each condition.
When I tried to use the same code for it, I did not get any error, but I also did not get the heatmap.
So, my question is can I make a distance heatmap for 4 samples- 2 being one condition, other 2 being controls or not?
If, yes, how should I change the code? Given I will use the correct data.

Thank you for reading my post.
I hope to get your help.

Best wishes,


modified 2 hours ago



2 hours ago


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