## User: 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 >
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... 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
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... Thank you very much for your answer, I will use kegga to get a go enrichment analysis too. ...
written 12 weeks ago by matrs10
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... Thank you for your answers, I did use goseq. ...
written 12 weeks ago by matrs10
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... 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
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... 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 ...
written 12 weeks ago by matrs10 • updated 12 weeks ago by Gordon Smyth39k
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... 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
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... 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 ...
written 3 months ago by matrs10
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... 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
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... 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' ...
written 20 months ago by matrs10

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