User: umeshtanwar2

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umeshtanwar230
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2 years, 1 month ago
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Posts by umeshtanwar2

<prev • 37 results • page 2 of 4 • next >
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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 22 months ago by umeshtanwar230
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Comment: C: Running GSEA for DEGs
... Yes, its Arabidopsis. ...
written 22 months ago by umeshtanwar230
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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 22 months ago by umeshtanwar230
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Comment: C: Running GSEA for DEGs
... Thank you for the response. These are the official gene symbols for Arabidopsis. ...
written 22 months ago by umeshtanwar230
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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 22 months ago by umeshtanwar230 • updated 22 months ago by Prakash2.1k
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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 22 months ago by umeshtanwar230
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Comment: C: DESeq2: Differential gene expression
... Thank you a lot @i.sudbery. This was really very helpful. ...
written 22 months ago by umeshtanwar230
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Comment: C: DESeq2: Differential gene expression
... Thank you so much @ i.sudbery. ...
written 23 months ago by umeshtanwar230
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DESeq2: Differential gene expression
... Hi, I am working on RNA-Seq data for Arabidopsis plant. I have samples from 4 genotypes (A, B, C, D), Untreated and after treatment, with 3 replicates for each. I used STAR for alignment and obtained count.txt file by using featureCounts. Now I am doing the DGE analysis by DESeq2. My coldata looks l ...
R rna-seq written 23 months ago by umeshtanwar230 • updated 23 months ago by swbarnes29.6k
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(Closed) DESeq2: Differential gene expression
... Hi all I am working on the RNAseq data of Arabidopsis thaliana. I have done the differential gene expression analysis by using DESeq2. Now I have a list of DE genes (gene ID) in csv file. How can I have the names and description of the genes in my DE genes results file? My file looks like this: ...
rna-seq written 24 months ago by umeshtanwar230

Latest awards to umeshtanwar2

Popular Question 17 months ago, created a question with more than 1,000 views. For STAR for Genome Index and Alignment
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2: Differential gene expression
Popular Question 17 months ago, created a question with more than 1,000 views. For Running GSEA for DEGs

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