## User: ATpoint

ATpoint10
Reputation:
10
Status:
New User
Location:
Germany
Website:
https://www.biostars.o...
Last seen:
1 week, 3 days ago
Joined:
1 year, 10 months ago
Email:
a*********@gmail.com

Wet-lab biologist by training, wannaba computational biologist.

Biostars Mod: ATpoint

#### Posts by ATpoint

<prev • 16 results • page 1 of 2 • next >
0
56
views
0
... Just for the record, I suggested to cross-post this question here at BioC which originally was posted at [Biostars][1] a few weeks ago. [1]: https://www.biostars.org/p/370025/#381520 ...
written 4 weeks ago by ATpoint10
2
198
views
2
... Thank you both for the outstanding responsiveness to questions and issues. Can you move Aaron's comment to answer so it is the toplevel answer? ...
written 5 weeks ago by ATpoint10
2
198
views
2
... Maybe add a short comment to the tximport vignette referencing the suggestions from Aaron below. Using the corrected counts for things like clustering etc. is standard so I was actually surprised no one asked this before (by best knowledge, maybe I missed the respective threads). ...
written 6 weeks ago by ATpoint10
1
90
views
1
... Cross-posted on [Biostars][1] as suggested by Aaron. [1]: https://www.biostars.org/p/379520/ ...
written 6 weeks ago by ATpoint10
2
198
views
2
... Thanks Aaron, I think that should do it. If you move your comment to answer I can accept it. For completeness, here is the code I used: ## convert DGElist to SummarizedExperiments given a DGElist "y" from the code in toplevel question library(csaw) se <- SummarizedExperiment(assays ...
written 6 weeks ago by ATpoint10
2
198
views
2
... This I understand but how about obtaining normalized counts for non-GLM applications like clustering or checking normalization efficiency by MA plots. Can you use the offsets for those, too? ...
written 6 weeks ago by ATpoint10
2
198
views
2
... I imported a set of salmon quantifications into R with tximport default settings and exactly used the code on the manual page for [tximport][1] to prepare data for use with edgeR. The result is a DGElist with the offsets for the downstream DGE analysis. Issue: The DGElist (y\$samples) do ...
written 6 weeks ago by ATpoint10 • updated 6 weeks ago by James W. MacDonald50k
1
141
views
1
... Dear Michael, I think there is a little flaw in the source code of lfcShrink with DESe2 version 1.22.2. Given one wants to turn off the svalue calculation one would set svalue=F. Still in the code if one sets type="apeglm" the svalue will in any case be turned on without respecting the value ...
written 10 weeks ago by ATpoint10 • updated 10 weeks ago by Michael Love24k
1
305
views
1
... Thank you. Just out of interest, because I encountered this problem also on a different and unrelated dataset with larger sample sizes, suggesting that this is a rather general issue when n becomes large. Do you plan to make changes in future versions of apeglm to compensate for this issue interna ...
written 5 months ago by ATpoint10
1
222
views
1
... You should at least provide the MA plot and some data to reproduce what you've stated in the question. The DESeq2 object saved in a rdata file would be an option. ...
written 8 months ago by ATpoint10

#### Latest awards to ATpoint

Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.

Content
Help
Access

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