User: tarun2

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tarun20
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Posts by tarun2

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Comment: C: DESEq2: the use of interaction term and grouping with different betaPrior argume
... Hi Michael, Thank you for always responding and for the suggestions. Indeed, I'm stuck on version 1_14 as we speak. A brief follow-up question on the result generation using the grouping argument though. Is it correct how I inferred each of the contrast that I generated based on the bold heading t ...
written 7 months ago by tarun20
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DESEq2: the use of interaction term and grouping with different betaPrior arguments in older version of DESEq2
... Hi Michael, I have questions regarding the use of interaction term versus grouping with different betaPrior arguments using version 1_14_1. I'm still using DESEq2_1.14.1. I've been working on differential expression analysis of drought-tolerance in rice. I have 2 genotypes (tolerant and susceptibl ...
deseq2 betaprior interaction term multiple groups written 7 months ago by tarun20 • updated 7 months ago by Michael Love20k
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Comment: C: DESeq2: betaPrior changes significance dramatically
... Hi Michael, Sure. apologies for posting it here. ...
written 7 months ago by tarun20
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Comment: C: DESeq2: betaPrior changes significance dramatically
... Hi Michael, I have somewhat related questions regarding this post. I'm still using DESEq2_1.14.1. 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, ...
written 7 months ago by tarun20
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Principle in selecting the "appropriate" merging value for module generation
... To the developers, I have an RNA-Seq data from a reproductive-stage drought stress in rice. I have 2 genotypes (tolerant and sensitive) and 2 conditions (drought and well-watered) with 4 replications each. Basically, a 2x2 factorial experiment with 4 replications thus having 16 samples. I am workin ...
wgcna coexpression module mergecutheight written 8 months ago by tarun20
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Comment: C: DESeq LRT test and construction of Co-expression network
... Dr. Langfelder, I have been doing WGCNA getting an assistance from a specialist. I have a transcriptomics data on drought tolerance in rice at reproductive-stage. I have 2 genotypes (tolerant and sensitive) and 2 conditions (drought and non-stress) with 4 replications each. basically a 2x 2 factori ...
written 8 months ago by tarun20
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Comment: C: design versus interaction term similarities and/or differences?
... Sorry for the confusion and unclear questions Michael. Probably, what I'm trying to ask is would the above codes be sufficient enough to run a one-way ANOVA?   ...
written 9 months ago by tarun20
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Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
... To the developers, I am trying to run a complete pathway analysis on oryza sativa japonica (osa) using the package GAGE and Pathview but I ran into problems as indicated in the title. I am trying to run the codes as indicated on the tutorials as follows: deseq2.fc=res.05_NILD_SWAD$log2FoldChange ...
gage pathview rna-seq gage package written 9 months ago by tarun20 • updated 9 months ago by Luo Weijun1.4k
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Comment: C: design versus interaction term similarities and/or differences?
... Thanks, Michael. So is there any other way to do ANOVA after transformation? Or the codes above would be the one that DESEq2 users can use? Or is there any other way that DESEq2 can employ filtering by mean expression or variance after transformation? Please advise. Sincerely, Asher ...
written 9 months ago by tarun20
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Comment: C: design versus interaction term similarities and/or differences?
... Thank you as always Michael. I would also like to ask if the following codes will address testing for overall difference across the groups like oneway-ANOVA? dds.ANOVA<-DESeq(dds, test="LRT", reduced = ~1, parallel = TRUE) res.anova <- results(dds.ANOVA) We want to select genes for WGCNA a ...
written 9 months ago by tarun20

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Popular Question 7 months ago, created a question with more than 1,000 views. For Transcript level differential expression analysis

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