User: Sri Dewi

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Sri Dewi0
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Posts by Sri Dewi

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Comment: C: WGCNA module Eigengene PC1 and expression correlation
... Sorry for the broken link, hopefully it will work this time. https://cdn1.imggmi.com/uploads/2019/11/28/9fa736504f4c1eb2207db40a262f4091-full.png And also sorry for the confusion, what I meant was the normalized counts (RPKM). But I did found out the problem with my code, instead of using `signed` ...
written 14 days ago by Sri Dewi0
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WGCNA module Eigengene PC1 and expression correlation
... Hi, I am currently analyzing a small RNAseq data with 10 biological replicates for each 3 different timepoints (time1, time2, time3) from a mouse data. Firstly I mapped and quantified the data with miRDeep2 and proceed the counts data with DESeq2. As suggested I used `varianceStabilizingTransform ...
deseq2 wgcna rna-seq written 15 days ago by Sri Dewi0
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Comment: C: order of factors
... You are right, if I change the comparison order/level only in the `results()` I got the same list only with opposite values and I think this is due to different statistical values in between before `results()`? But this also got me thinking, which condition should then always be used for the baseli ...
written 11 weeks ago by Sri Dewi0
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Comment: C: order of factors
... Hi Michael, thanks for the quick response. Sure I can post it here library(DESeq2) library(data.table) library(vsn) library(ggplot2) library(gplots) library(clusterProfiler) library(ReactomePA) library(VennDiagram) library(plyr) library(WGCNA) first_c ...
written 11 weeks ago by Sri Dewi0
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Comment: C: order of factors
... Hi Michael, I am honestly still confused regarding the comparison order of DESeq2. If I compare my samples with: results(dds, contrast=c("condition", "non_treated", "treated"), pAdjustMethod="BH") I got a list of 1042 DEGs, but if I change the comparison order to: results(dds, contrast= ...
written 11 weeks ago by Sri Dewi0

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