Problem with the HeatMap - it is empty

[mvukk]

Dear all,

I am plotting WGBS data over predefined regions. This is command I used:

computeMatrix reference-point -R regions.bed \
               -S DNA_3.bw \
                    DNA_4.bw \
                    DNA_1.bw \
                    DNA_2.bw \
                --outFileName matrix.gz \
                --referencePoint center \
                --binSize 100 \
                -b 5000 -a 5000
plotHeatmap --matrixFile matrix.gz \
                --missingDataColor "#FFF6EB" \
                --colorMap jet \
                --yMin 0 --yMax 100 \
                --outFileName HeatMap.pdf

and this is the HeatMap I get:

(profile plot looks as expected but heatmap is empty)

Also if I do remove yMin and yMax and leave default colorMap, I get same result just black heatmap:

plotHeatmap --matrixFile matrix.gz \
                  --outFileName HeatMap.pdf

Does anyone have suggestion, or can maybe point out what I am doing wrong?

Thank you,
Regards,
Maja

[dpryan79]

Is your data extremely sparse?

[mvukk]

It is WGBS (should be covering all CpGs) done for mouse genome. It is not continues, I do have NA values in my matrix, but I would not say it is extremely sparse.

[dpryan79]

That's quite sparse, you're not going to end up with a nice heatmap of BS-seq data.