User: matrs

gravatar for matrs
matrs10
Reputation:
10
Status:
New User
Location:
Last seen:
4 days, 9 hours ago
Joined:
1 year, 7 months ago
Email:
j**********@ug.uchile.cl

Posts by matrs

<prev • 9 results • page 1 of 1 • next >
0
votes
2
answers
238
views
2
answers
Comment: C: goana and "No annotated genes found in universe" even with Entrez gene ids
... I see, I never use `genes=` in this step: `dglst <- DGEList(y, genes = annot)` What happens is that I'm coming from `salmon` transcript counts -->`tximport` gene level -->`edgeR`. So when I go from transcripts level to gene level, I use the direct translation from SGD (same as ensembl) tr ...
written 12 weeks ago by matrs10
0
votes
2
answers
238
views
2
answers
Comment: C: goana and "No annotated genes found in universe" even with Entrez gene ids
... Thank you very much for your answer, I will use `kegga` to get a go enrichment analysis too. ...
written 12 weeks ago by matrs10
0
votes
2
answers
238
views
2
answers
Comment: C: goana and "No annotated genes found in universe" even with Entrez gene ids
... Thank you for your answers, I did use `goseq`. ...
written 12 weeks ago by matrs10
0
votes
2
answers
238
views
2
answers
Comment: C: goana and "No annotated genes found in universe" even with Entrez gene ids
... That's a point where some of my confusion comes, my DGLRT object doesn't have a `genes` item and from the manual I don't get that I have to create it. Is It supposed to have a `genes` item? ``` > names(dgelist_qltest) [1] "coefficients" "fitted.values" "deviance" "m ...
written 12 weeks ago by matrs10
6
votes
2
answers
238
views
6 follow
2
answers
goana and "No annotated genes found in universe" even with Entrez gene ids
... I'm using `edgeR` to perform a a RNA-seq differential expression analysis with *S. cerevisiae* samples and then trying to use `goana`. My genes ids are from ensembl so **I added a column with entrezgene ids** to the `DGELRT` object, which is coming from the `glmQLFTest` function. I'm not sure wher ...
edger goana written 12 weeks ago by matrs10 • updated 12 weeks ago by Gordon Smyth39k
0
votes
1
answer
120
views
1
answers
Comment: C: Disagreement between results of two 'getBM' queries
... Thanks for your answer, i'll keep in mind this, to query as few as possible attributes at once. ...
written 3 months ago by matrs10
1
vote
1
answer
120
views
1
answer
Disagreement between results of two 'getBM' queries
... `R version 3.6.0 (2019-04-26)` `Platform: x86_64-pc-linux-gnu (64-bit)` `BiocManager 1.30.4` `biomaRt_2.40.3` (latest) I've been working with the `biomaRt` package to get mappings between different organizations and I noticed something that, to me, seems like a bug, but I'm not sure. I'm tryi ...
biomart written 3 months ago by matrs10
0
votes
2
answers
527
views
2
answers
Answer: A: how to get the last version of tximport
... Thanks, it worked as expected. I didn't see the last part of the guide before, so i missed  the sessionInfo() output, my fault.  If anybody wants to try the last version: library(devtools) options(unzip = 'internal') install_github("mikelove/tximport") By the way, there is a small mistake in t ...
written 20 months ago by matrs10
2
votes
2
answers
527
views
2
answers
how to get the lastest version of tximport
... packageVersion("tximport") [1] '1.6.0' I'm following this guide and when testing with a single table from stringtie, I get the following error: txi <- tximport(files, type = "stringtie", tx2gene = tx2gene) Error in match.arg(type, c("none", "salmon", "sailfish", "kallisto", "rsem")) : 'arg' ...
stringtie tximport written 20 months ago by matrs10

Latest awards to matrs

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 223 users visited in the last hour