User: tarun2

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tarun20
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Posts by tarun2

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Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... Thanks, Michael, That is my understanding as well based on your paper and reading on the DESEq2 community.  So using either rlog or vst will not (greatly) affect differential expression analysis at all and generating the same number and list of differentially expressed genes is okay and not at all ...
written 18 hours ago by tarun20
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Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... Hi Michael, I'm having similar list and numbers of DEG's. So I'm doing differential expression analysis on drought tolerance at reproductive-stage drought stress with two contrasting genotypes and two conditions with 4 replications. My codes are as follows; Please and kindly comment if there's so ...
written 1 day ago by tarun20
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Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... Thanks for the clarifications. That brings me to an additional question, will the number and list of differentially expressed genes generated changes if we use either rlog or vst using the BLIND = FALSE argument or will it be the same?  Please advise. ...
written 3 days ago by tarun20
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Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... That being said, being a novice in differential expression analysis and have been following DESEq2 pipeline, is there a better transformation method? Or when does rlog is more superior vst and vice versa if that's even a point? Many thanks. ...
written 5 days ago by tarun20 • updated 5 days ago by Michael Love15k
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sample removal after clustering
... To the developers,   I'm a novice R user and new to the expression profiling analysis as well. I am trying to do a differential expression analysis on a 2x2 factorial experiment (2 drought contrasting genotypes and 2 contrasting conditions) with 4 replicates per sample to have a 16 experimental u ...
deseq2 rlog transformation written 5 days ago by tarun20 • updated 5 days ago by Michael Love15k
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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 4 months ago by tarun20 • updated 4 months 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 5 months 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 5 months 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 5 months 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 5 months ago by tarun20

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