User: tarun2

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tarun20
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Posts by tarun2

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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 14 days 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 15 days 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 8 weeks 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 8 weeks ago by tarun20 • updated 7 weeks 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 8 weeks 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 8 weeks ago by tarun20
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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 8 weeks 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 8 weeks ago by tarun20 • updated 8 weeks ago by Michael Love17k
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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 12 weeks 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 12 weeks ago by tarun20

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