Heatmap normalization
From Array Suite Wiki
Array studio provide several different ways to normalize the heatmap, they are:
Method | Detail |
None | No normalization |
Center | Each cell subtracts its row mean |
RobustCenter | Each cell subtracts its row median |
CenterScale | Each cell subtracts it row mean and then scales by row normalization factor so the row has mean 0 and variance 1 |
RobustCenterScale | Each cell subtracts it row median, and then scales by row MAD (Median absolute deviation) |
CenterByAllValue | Each cell subtracts the mean of the whole data set. |
RobustCenterbyAllValue | Each cell subtracts the median of the whole data set. |
CenterScaleByAllValue | Each cell subtracts the overall mean and then scales by overall normalization factor so the whole data set has mean 0 and variance 1 |
RobustCenterScaleByAllValue | Each cell subtracts the overall median and then scales by overall MAD. |
Note that when the change of normalization of the heatmap only change the color of the map, but it will not affect the underlying table values. Also, for the normalization methods: Center, RobustCenter, CenterScale and RobustCenterScale, a row represents a gene.