Question: Z score in RNAseq
0
gravatar for rob.costa1234
6 months ago by
rob.costa1234150
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 https://www.nature.com/articles/nature24489 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 • 884 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe21k • written 6 months ago by rob.costa1234150
3
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k 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).

Kevin

ADD COMMENTlink modified 6 weeks ago • written 6 months ago by Kevin Blighe21k
1

Great! I was missing K means point.

ADD REPLYlink written 6 months ago by rob.costa1234150
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