User: rodrigo.duarte88
rodrigo.duarte88 • 20
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Posts by rodrigo.duarte88
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... Hi all
I apologise for what may be a very stupid question, but I am currently trying to interpret my WGCNA results, and I could not find anything online about what the following means.
I am interested in this module turquoise ([Module-trait relationship table][1]). There is a fairly weak correlati ...
written 4 weeks ago by
rodrigo.duarte88 • 20
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... Thanks, Michael! I just wanted to confirm that because I was working with two dds objects (one created based on a tximport object, and the other one imported using a count matrix). When I transform the dds objects using the vst function, it prints a message (for the dds object created using tximport ...
written 4 weeks ago by
rodrigo.duarte88 • 20
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Comment:
C: ComBat with multiple batches
... A more detailed explanation as to why one shouldn't run Combat like this
https://support.bioconductor.org/p/93457/#93467 ...
written 5 weeks ago by
rodrigo.duarte88 • 20
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Comment:
C: ComBat with multiple batches
... I also want to use Combat to adjust my data for multiple confounders, but I am not sure this sounds right. What if potential confounders were interacting, for example age and medication? ...
written 5 weeks ago by
rodrigo.duarte88 • 20
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... Link is down, unfortunately. ...
written 7 weeks ago by
rodrigo.duarte88 • 20
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... Hi Michael
Hope things are well with you! When outputting normalized counts from a dds object like this:
dds <- estimateSizeFactors(dds);
counts(dds, normalized=TRUE)
... will these counts be normalized to gene length, taking into consideration that counts were imported using tximport ...
written 7 weeks ago by
rodrigo.duarte88 • 20
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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 6 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 6 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 8 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 8 months ago by
rodrigo.duarte88 • 20
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