Changes between Version 5 and Version 6 of SOPs/clusteringMatrixHeatmap

Timestamp:

08/31/21 23:47:16 (3 years ago)

Author:

thiruvil

Comment:

--

SOPs/clusteringMatrixHeatmap

@@ -47 +47 @@
   * We always prefer log2 ratios rather than levels (like RPKM).  Ratios provide more information to the clustering algorithm, and the result (as a heatmap) includes clearer visual cues of changes (since one has a range of positive and negative values, instead of just a range of positive values).  In that case, however, you often have a choice of the reference(s) for your ratios, whether it's another sample or a median of all samples.
   \\
-  \\ Note: To create a heatmap using z-scores, log2-transform the expression values (e.g. normalized counts, FPKM, etc.) and then calculate the z-scores.  In R, the [[https://stat.ethz.ch/R-manual/R-patched/library/base/html/scale.html | scale]] function can be used.
+  \\ Note: To create a heatmap using z-scores, log2-transform the expression values (e.g. normalized counts, FPKM, etc.) and then calculate the z-scores.  In R, the [[https://stat.ethz.ch/R-manual/R-patched/library/base/html/scale.html | scale]] function can be used after transposing the data, by default scale calculates column-wise z-score not row-wise.
 2 - How to normalize or scale the data, if necessary?
   * Same as for general other analyses of this sort of data, and you probably want to do this before any filtering (so do it on all genes, rather than selected genes).  Log2 transformation of ratios is almost always a good idea.