catchSalmon
1
0
Entering edit mode
Ina Hoeschele ▴ 620
@ina-hoeschele-2992
Last seen 9 months ago
United States

Hi Gordon, in the absence of any description of catchSalmon, I have inferred from the code precisely what it does. Would you be willing to provide an explanation (1) for the definition of the overdispersion coefficient (sum of squares over row mean), (2) for the prior (use of qf and median) and (3) why it is ok to input the counts scaled with the transcript-wise overdispersion coefficients into edgeR, voom etc.. Thank you. Comments from others to whom this is obvious are also much appreciated.

catchSalmon edgeR • 256 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 2 hours ago
WEHI, Melbourne, Australia

See catchSalmon for tx-level DE

This forum is to provide help with the software syntax and I can help you with that if you have any questions about it. I prefer however to use the refereed literature for publishing mathematical justifications or comparative studies. I understand you might not want to use catchSalmon until it is supported by a published paper, and that's fine.

ADD COMMENT

Login before adding your answer.

Traffic: 261 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6