Question: Z score in RNAseq
gravatar for rob.costa1234
2.6 years ago by
United States
rob.costa1234250 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 • 4.3k views
ADD COMMENTlink modified 2.6 years ago by Kevin Blighe61k • written 2.6 years ago by rob.costa1234250
gravatar for Kevin Blighe
2.6 years ago by
Kevin Blighe61k
Kevin Blighe61k 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 (edit: see zFPKM R package). The point again, however, is that the Z-score transformation is generally for visualisation in RNA-seq studies, or for other downstream analyses outside of the standard differential expression.

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 modified 2.2 years ago • written 2.6 years ago by Kevin Blighe61k

Great! I was missing K means point.

ADD REPLYlink written 2.6 years ago by rob.costa1234250
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: 994 users visited in the last hour