Question: fold change in Ballgown
0
gravatar for Fawzi Yassine
6 days ago by
Fawzi Yassine0 wrote:

What is the formula that Ballgown uses to calculate fc? Does it use a log? thank you,

rna-seq • 80 views
ADD COMMENTlink modified 3 days ago • written 6 days ago by Fawzi Yassine0
1

There are several references:

Question: How fold change is calculated in Ballgown?

https://support.bioconductor.org/p/91092/

https://support.bioconductor.org/p/77144/

Fold changes for different gene expression datasets?

Other details that may be useful:

ballgown has "." as Gene Names

ballgown installation problem

Error while loading the data structrure in the ballgown tool

Ballgown library load

R-library https://digibio.blogspot.com/2017/10/rnaseq-ballgown-analysis.html

some example: https://rdrr.io/bioc/ballgown/man/stattest.html

And see the right panel for more posts.

ADD REPLYlink modified 6 days ago • written 6 days ago by natasha.sernova3.3k

hi, The stattest doc says fc=llog(expression+1), while forums say fc=wt/ko if the groups are wt and ko.

ADD REPLYlink written 3 days ago by Fawzi Yassine0

hi, The stattest doc says fc=llog(expression+1), while forums say fc=wt/ko if the groups are wt and ko.

ADD REPLYlink written 3 days ago by Fawzi Yassine0
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 2.3.0
Traffic: 643 users visited in the last hour