Hi there, I am really wrapping my head around a thing that I may have forgotten. Essentially, I have different results (i.e. rld ones) that I will use in my heat map that changes according to the number of samples I consider. I am wondering why this is happening. Given the fact I am sure I haven't explained myself clearly, I will try to paraphrase what I have just said:
I want to generate 2 heat maps: one, from the main comparison I am interested (6 samples) second one, containing results from all samples in my dataset (6 samples as before + 2)
by doing this, in both conditions:
dds <- DESeqDataSetFromTximport(txi.kallisto.tsv, table, ~condition) dds <- DESeq(dds) rld <- rlog(dds, blind=FALSE) top_genes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 100) mat <- assay(rld)[ top_genes, ]
I obtain different counts for the same genes in the 2 aforementioned conditions. Is this due to the fact that regularised logarithmic transformation is different according to the number of samples in the dataset?