Hello!

I am in the process of making different heatmaps of ChIPseq bigwig files from the same publication to check chromatin binding patterns, and had a question regarding the zMin and zMax. I am not using the entire mm10 genome as an input, but rather a list of genes my colleagues generated that are of interest to our biological question.

To make my example more general, my groups of bigwig files are group 1 and group 2, and I did the following:

1. computeMatrix with the following parameters, noting that the only differences are the input bw files

computeMatrix reference-point \
-b 10000 -a 10000 \
-R induction.gtf \
-S K27ac-5uM-rep1.bw K27ac-5uM-rep2.bw K27me3-5uM-rep1.bw K27me3-5uM-rep2.bw \
--skipZeros \
-o matrix-induction-chromreg.gz \
-p 6 \
--outFileSortedRegions regions-5uM-induction-chromreg.bed

computeMatrix reference-point \
-b 10000 -a 10000 \
-R induction.gtf \
-S Cttnb1-5uM-rep1.bw Cttnb1-5uM-rep2.bw  Lef1-5uM-rep1.bw Lef1-5uM-rep2.bw Tcf7-5uM-rep1.bw Tcf7-5uM-rep2.bw \
--skipZeros \
-o /project/nilslind_369/cfausto/distal_genes/output/5uM-CHIR/10kb/matrix-induction-bcattarget.gz \
-p 6 \
--outFileSortedRegions /project/nilslind_369/cfausto/distal_genes/output/5uM-CHIR/10kb/regions-5uM-induction-bcattarget.bed

2. Two separate plotHeatmaps using the different matrix files generated, but the same zMin and zMax

plotHeatmap -m matrix-induction-bcattarget.gz \
-out 5uM-induction-bcattarget-heatmap.png \
--colorMap RdBu \
--zMin -3 --zMax 5 \
--whatToShow 'heatmap and colorbar' \
-T '5uM Induction' \
--kmeans 6 \
--outFileSortedRegions 5uM-induction-bcattarget-clusters.bed

plotHeatmap -m matrix-induction-chromreg.gz \
-out 5uM-induction-chromreg-heatmap.png \
--colorMap RdBu \
--zMin -3 --zMax 5 \
--whatToShow 'heatmap and colorbar' \
-T '5uM Induction' \
--kmeans 6 \
--outFileSortedRegions 5uM-induction-chromreg-clusters.bed

By doing this, can I assume my zMin and zMax are comparable across the two different heatmap png generated?