User: rodrigo.duarte88
rodrigo.duarte88 • 20
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Posts by rodrigo.duarte88
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... Just in case someone stumbles upon this in the future, too.... I had help from a colleague and created the required annotation for GARFIELD in R using the short script below:
library(data.table)
dbsnp<-fread("eQTL_positions.bed", skip = 1)
for(chr in 1:22){
tmp<- ...
written 4 months ago by
rodrigo.duarte88 • 20
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... Hi all,
I think I may have an impossible question here, but if by any chance any of you has used the EMBL-EBI tool 'Garfield' (https://www.ebi.ac.uk/birney-srv/GARFIELD/), could you please advise? Garfield is available as a bunch of shell scripts or as an R package, but I am having an issue specifi ...
written 5 months ago by
rodrigo.duarte88 • 20
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... I had the same error, and removing low count genes from counts table (as suggested in sva tutorial, https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf) worked for me.
...
written 6 months ago by
rodrigo.duarte88 • 20
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... Oops, sorry about that! To be fair, I think am going to try "sva", looks like there's more documentation for that one. Thanks, Martin! ...
written 6 months ago by
rodrigo.duarte88 • 20
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... Fantastic! Thanks, Michael! Just one more quick question (for peace of mind): I am using the "~1" design to create this dds object to extract the normalised counts, since I have no groups, right? ...
written 6 months ago by
rodrigo.duarte88 • 20
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... Hi all,
I am trying to use PEER in R (on conda) to identify hidden confounders in the raw counts of my RNA-seq experiment. I am following their tutorial ( https://github.com/PMBio/peer/wiki/Tutorial ), but without much luck, and there's not much help available unfortunately. Anyone used this tool b ...
written 6 months ago by
rodrigo.duarte88 • 20
• updated
6 months ago by
Martin Morgan ♦♦ 23k
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Comment:
C: Handling missing data, DESeq2
... Looks like you have 3 time points, but how many samples for each time point do you have? I think that as long as you have at least 3 samples per time point, you should be fine? ...
written 7 months ago by
rodrigo.duarte88 • 20
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... Dear all,
I've got a naive question for you, and I would really appreciate your thoughts.
I found some transposable elements (TE) that were differentially expressed in a certain tissue, based on a case-control analysis of RNA-seq data using DESeq2, and a custom-made annotation for TEs. Now, **I w ...
written 7 months ago by
rodrigo.duarte88 • 20
• updated
7 months ago by
Michael Love ♦ 24k
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Comment:
C: Subsetting a tximport object
... Many thanks, Michael! This is super useful, as usual!
...
written 7 months ago by
rodrigo.duarte88 • 20
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Comment:
C: Subsetting a tximport object
... Hi [James][1],
I was wondering if you know how I could remove samples from the tximport object which are contained in a list of outliers? Thanks!
[1]: https://support.bioconductor.org/u/5106/ ...
written 7 months ago by
rodrigo.duarte88 • 20
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