Question: Understanding NextMaSigPro, regression fit and stepwise regression
0
gravatar for jelisaveta.jeki.djordjevic
21 months ago by

Hi,

I wanted to use NextMaSigPro package to study dynamics of gene expression over development.  As part of this study is descriptive, I wanted to extract the information on how many genes increase expression over time, or decrease, or stay flat, etc.

To check this, I made a single series (only females) design matrix, with three replicates for each of the three-time points (quadratic regression). Then, I called p.vector() to get a regression fit for each gene. Out of 15 500 genes, 10 519, are significant. As my only variables, in this case, are Time and Time2, does this mean that 10 519 genes, change expression over time?

If that is the case, what exactly am I looking when I do stepwise regression, for variable selection? After stepwise regression, 4217 out of 10 519 genes are significant.

I hope that I am clear enough.

Thanks for the help,

Jelisaveta

rnaseq timecourse masigpro • 395 views
ADD COMMENTlink written 21 months ago by jelisaveta.jeki.djordjevic0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 110 users visited in the last hour