Heatmaps of RNA SEQ data

Question

This is my first time in working with RNA SEQ data and I have some problems with heatmap

My data is as follows Data

I wanted to create a heatmap to show tissue specific expression and tried the following

 rownames(data)<-data$IDS
 data<-data[,-1]
 hmcol = colorRampPalette(brewer.pal(9, "GnBu"))(100)
 heatmap.2(as.matrix(data), col = hmcol, trace="none")

The values in the data do not match to the color key in the heatmap.Could someone please correct where am wrong?

Answer 1

It seems that you just have alot of small values and few extremely large values. Hence, the color key is correct (See the histogram in the color key) but the low (grey) values just dominate the picture. You could try to plot the values on a logarithmic scale.

Maybe try something like:

heatmap.2(log2(as.matrix(data) + 1), col = hmcol, trace="none")

Answer 2

Have you analyzed your DE? after filtration and normalization steps and finaly DE try it again on your expressed genes (also for PCA).