Question: Z score in RNAseq
gravatar for rob.costa1234
3 months ago by
United States
rob.costa1234150 wrote:

I am trying calculate Z score of expression from RANseq dataset Ultimate goal is to generate similar figure as in Supplementary Fig 2 B and C of I read a discussion (calculate z-score from rpkm values.) that Z score may not be useful in showing the expression changes. Are there any additional steps after simple calculation of z score that may be needed to generate a matrix close to above Fi2 and C above? Any thoughts or suggestions what should be best way to represent change in gene expression using Z score

zscore rna-seq • 498 views
ADD COMMENTlink modified 3 months ago by Kevin Blighe14k • written 3 months ago by rob.costa1234150
gravatar for Kevin Blighe
3 months ago by
Kevin Blighe14k
London / Brazil
Kevin Blighe14k wrote:

Gene expression values are generally converted to Z-scores for visualisation purposes, like, in heatmaps. The differential expression analysis itself is performed on normalised counts, prior to log and/or Z-score transformation. Any data can be converted to Z-scores, including FPKM values. The point again, however, is that the Z-score transformation is purely for visualisation.

I don't see any major steps that need to be further applied after Z-score transformation for Figure 2B. Figure 2C, however, looks like the plotting of the first 3 dimensions after k-means clustering (hope that we're looking at the same figures).


ADD COMMENTlink written 3 months ago by Kevin Blighe14k

Great! I was missing K means point.

ADD REPLYlink written 3 months ago by rob.costa1234150
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 837 users visited in the last hour