Question: Is logFC a log2 fold change or some other base in scran::findMarkers
1
gravatar for Chris Conley
6 weeks ago by
Huntsman Cancer Institute
Chris Conley0 wrote:

Aaron, I searched ?scran::pairwiseTTests as well as the code on GitHub but could not find out whether the lfc argument and corresponding output column prefixed with logFC was log2 or natural log. I assume that it is base 2 as the limma output. Thanks in advance! Chris

scran • 74 views
ADD COMMENTlink modified 6 weeks ago by Aaron Lun24k • written 6 weeks ago by Chris Conley0
Answer: Is logFC a log2 fold change or some other base in scran::findMarkers
2
gravatar for Aaron Lun
6 weeks ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

It's the same base as the log-transformation that was used to create the assay.type. If you were following the standard workflow using, e.g., scater::normalize, then yes, this would be base 2. If you did your own thing, then it's whatever base you used to compute the input x. I'll mention this explicitly in the documentation.

ADD COMMENTlink written 6 weeks ago by Aaron Lun24k

Thanks, I give a strong endorsement of the simple single cell workflow.

ADD REPLYlink written 6 weeks ago by Chris Conley0
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: 118 users visited in the last hour