User: rodrigo.duarte88

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Posts by rodrigo.duarte88

<prev • 19 results • page 1 of 2 • next >
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WGCNA: correlations module-traits, and module membership-gene significance
... 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 ...
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Comment: C: [DESEQ2] How to access the normalized data of a DESeqDataSet
... 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.duarte8820
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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.duarte8820
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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.duarte8820
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Comment: C: WGCNA automatic vs manual network creation
... Link is down, unfortunately. ...
written 7 weeks ago by rodrigo.duarte8820
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Comment: C: [DESEQ2] How to access the normalized data of a DESeqDataSet
... 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.duarte8820
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Answer: A: How to run the annotation tool for GARFIELD v2: garfield_annotate_uk10k.sh
... 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.duarte8820
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How to run the annotation tool for GARFIELD v2: garfield_annotate_uk10k.sh
... 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 ...
unix shell garfield awk embl-ebi written 6 months ago by rodrigo.duarte8820
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Comment: C: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
... 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.duarte8820
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Comment: C: Using PEER to identify hidden confounders in RNA-seq data (not working)
... 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.duarte8820

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