[BioC] heatmap.2 function and the scale option

[john herbert]

Dear Bioconductors,
I am using the the heatmap.2 function to plot out a heatmap of 130
genes from Q-PCR expression.

If I plot them out scaling by row, I get a heatmap that looks a bit blotchy.

However, if I scale by column, the heatmap looks a lot better.

The clustering of samples is the same but I don't really know the
theory behind why column scaling looks better than row scaling.

Please can someone advise me on any theory behind this?

The data is in a matrix, like microarray, with columns of different
conditions and rows of genes.

Thank you,