User: tarun2

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tarun20
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Posts by tarun2

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What R version does systemPipeR runs
... To the developers, I was able to load and install systempiper in R version 3.1.2 yesterday. But today, since we transitioned to SLURM, we have R/3.2.5 and the newest versions. I was trying to install and load systempiper but I ran into some problems, there is no package systempiper and the batchjo ...
R systempiper batchjobs written 8 weeks ago by tarun20 • updated 8 weeks ago by Thomas Girke1.6k
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Comment: C: Unused argument of reader = read_tsv on R version 3.4.1
... Hi Michael, Dumb follow-up question here, I have a readr package installed (version 1.1.1) when I upgraded my R version to 3.4.1. Saying that "read_tsv will be used by default if readr package is installed" is for the older tximport version (1.2.0) and not for version 1.4.0? Because since I upgrade ...
written 12 weeks ago by tarun20
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Comment: C: Unused argument of reader = read_tsv on R version 3.4.1
... Hi Michael,  I would like to still use that argument as that's what works for me before on the previous R version. What version of tximport should I use for me to be able to use that argument again? And can I used that old version with the new version of R and Bioconductor that I installed? Thank ...
written 12 weeks ago by tarun20
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Comment: A: Unused argument of reader = read_tsv on R version 3.4.1
... To The Developers, I did re-install the R version 3.4.1. I did re-install the DESeq2 version 1.16.1 and tximport version 1.4.0 through the Bioconductor page as reflected on the session info below. However, I'm still getting the same error when running this command. > tx.all <- tximport(myfi ...
written 12 weeks ago by tarun20
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Unused argument of reader = read_tsv on R version 3.4.1
... To The Developers, I updated my R from version 3.3.2 to version 3.4.1 primarily so I can use the latest version of DESeq2 which is version 1.16.1 I'm using the tximport package to import transcript-level estimates. It was working before when I'm using R version 3.3.2 and version 3.3.2 but my DESeq ...
tximport written 12 weeks ago by tarun20
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DESeq2 version 1.16.1 installation and difference with version 1.14.1
... To the developers, I'm using DESeq2 version 1.14.1, and I want to upgrade to version 1.16.1, but I'm still stuck with version 1.14.1 I'm using R version 3.3.2 and Bioconductor version 3.4 (BiocInstaller 1.24.0). I tried doing the typical installation in R through the Bioconductor page, but to no av ...
deseq2 lfcshrink betaprior=true written 12 weeks ago by tarun20 • updated 12 weeks ago by James W. MacDonald45k
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DESeq2 function in interpreting the differential expression results in terms of higher order biological processes or molecular pathways
... Hi,   Does DESeq2 have a build in function for pathway analysis like Gene Ontology (GO) and KEGG or any pathway?   Thanks and best regards.   Sincerely, Asher ...
deseq2 pathway analysis written 6 months ago by tarun20 • updated 6 months ago by Michael Love14k
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Comment: C: DEGs generation parameters and specificities
... Hi Michael, I'm sorry if I may have confused you in detecting weak DE genes. Our goal is to identify differentially express genes. That's why I invoke the LFC threshold. And also the reason being adding the LFC threshold is that from your paper, "a statistical test against the conventional null hyp ...
written 7 months ago by tarun20
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Comment: C: DEGs generation parameters and specificities
... Hi Michael, Thank you so much for the advice. I did what you suggested This is how I go about it. Please and kindly comment if I did it correctly. colData <- data.frame(geno=rep(c("NIL","Swarna"),each=8),condition=rep(rep(c("Control","Drought"),each=4),times=2)) rownames(colData) <- colna ...
written 7 months ago by tarun20
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DEGs generation parameters and specificities
... I've been following DESeq2 vignette, manuals, and different posts/blog from DESeq2 community that I came up with my analysis. Apologies as this will be a lengthy post I have a 2x2 factorial experiment on drought tolerance in rice under reproductive stage with four biological replicates I have 2 ge ...
deseq2 design and contrast matrix results written 7 months ago by tarun20 • updated 6 days ago by Michael Love14k

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