I'm a beginner on RNAseq, so any help here would be amazing.

Just a quick explanation of the dataset, I have two genotypes (WT and KO), and four time points of treatment (four conditions). The important thing is that I have two experiments with the same conditions.

So, I've done DEseq for differential expression, included the batch effect, got the list of DE log2FC. This part is OK.

What I want now is to plot expression values (not the fold change) for each time point and genotype in a heatmap for example. My question is what is the ideal way to show that? Should I use the rlog normalized values from DEseq? If so, since I have 2 distinct experiments, I remove batch effect, right? What is the best way to do that?

I also have a TPM file generated using Kallisto that contains the counts for each experiment. I know it's not ideal to use it to compare between samples, but I want to use it to compare genes within a sample. However, again, to merge the values from the different experiments, I need to remove batch effect, right? How would I do that?

(By the way, I know there is a batch effect because plotting a heatmap using TPM, the samples in each experiment cluster together.)

If anyone can shed a light here, that would be super helpful. I'm going mad with this. Thank you