User: tarun2

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tarun20
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Posts by tarun2

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Comment: C: design versus interaction term similarities and/or differences?
... Hi Michael, Since we have two genotypes, one is very drought tolerant (IL) and the other is very drought susceptible (Swarna). The drought-tolerant genotype is a cross between an inbred line (tolerant) and the other genotype in the study (susceptible). There's a major QTL that is introgressed into ...
written 21 months ago by tarun20
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design versus interaction term similarities and/or differences?
... To the developers, I've been working on differential expression analysis of drought-tolerance in rice. I have 2 genotypes (tolerant and susceptible) and 2 conditions (drought and well-watered) with 4 replications each, essentially a 2x2 factorial experiment with 4 replications. One of my main obje ...
deseq2 anova design interaction term written 21 months ago by tarun20 • updated 21 months ago by Michael Love26k
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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 22 months 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 22 months 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 22 months 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 22 months ago by tarun20 • updated 22 months ago by Michael Love26k
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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 22 months ago by tarun20 • updated 22 months ago by Michael Love26k
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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 2.2 years ago by tarun20 • updated 2.2 years ago by Thomas Girke1.7k
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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 2.2 years 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 2.2 years ago by tarun20

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Popular Question 18 months ago, created a question with more than 1,000 views. For Transcript level differential expression analysis

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