User: umeshtanwar2

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umeshtanwar210
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Posts by umeshtanwar2

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Differential gene expression analysis by DESeq2
... Thank you very much Carlo. This is really very helpful. ...
written 11 weeks ago by umeshtanwar210
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Differential gene expression analysis by DESeq2
... Hi all, I am doing Differential Gene Expression Analysis using DESeq2. I have 8 samples in total (4 treated and 4 untreated) with 3 replicates of each. I am using the the code given below: library(DESeq2) dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~genotyp ...
deseq2 rna-seq lfcthreshold written 11 weeks ago by umeshtanwar210 • updated 11 weeks ago by Carlo Yague4.6k
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Comment: C: Running GSEA for DEGs
... I am not using the command line but GSEA Desktop Application. The format of these files looks different from the one you posted. I do not know from which source I can get the gene data sets for Arabidopsis. I could not find Arabidopsis on gsea/msigdb. Could you please suggest some link? Other thing ...
written 4 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Thank you Kevin, It is working now. I have downloaded the gene data sets files for Arabidopsis thaliana from the website [enter link description here][1]. Is this right to use that? It shows error when the GMT formatted file for all gene sets is uploaded. But works well when some of individual dat ...
written 4 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Thank you. I have used this code: rld <- rlogTransformation(dds) head(assay(rld)) hist(assay(rld)) write.table(assay(rld), file="gsea.txt") I obtained this file: > "A_m1" "A_m2" "A_m3" "A_t1" "A_t2" "A_t3" "B_m1" "B_m2" "B_m3" "B_t1" "B_t2" "B_t3" "C_m1" "C_m2" "C_m3" "C ...
written 4 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Yes, its Arabidopsis. ...
written 4 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Thank you @Kevin. I am new for this kind of analysis. In total I have 8 samples (4 treated and 4 untreated) with 3 replicates. countdata <- read.table("NewTotalCounts.txt", header=TRUE, row.names=1) countdata <- countdata[ ,6:ncol(countdata)] countdata <- as.matrix(countdata) ...
written 4 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Thank you for the response. These are the official gene symbols for Arabidopsis. ...
written 4 months ago by umeshtanwar210
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Running GSEA for DEGs
... Hi all, I am working on RNA-seq data of Arabidopsis plant. I have a list of Deferentially Expressed Genes obtained from DESeq2. Now I would like to do further analysis using GSEA. I prepared the rank file by using the code below: x <- read.csv("DEG-B_vs_A.csv") attach(x) x$fcSign=si ...
next-gen rna-seq written 4 months ago by umeshtanwar210 • updated 4 months ago by Prakash1.4k
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Comment: C: DESeq2: Differential gene expression
... Thank you so much @swbarnes2. I am more clear about interaction effects after reading this tutorial. ...
written 4 months ago by umeshtanwar210

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