User: manish20072013

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Posts by manish20072013

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RNAseq Analysis using RUVs
... I have three groups each have 4 replicates. The conditions for each group were same before preparing library and then sequencing. Now I have to analyse the read counts to find DE genes between Group1 vs Group2, Group2 vs Group3 and Group1 vs Group3. But I do not know whether to combine all the gro ...
R ruvs next-gen rna-seq written 2.1 years ago by manish200720130 • updated 23 months ago by Biostar ♦♦ 20
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How to generate heatmap for three groups
... I have three groups let's say C, L, and T, each with three replicates. I did comparison between C vs L, C vs T, and L vs T to find the Deferentially expressed genes in each compassion. I used RUVs package to find the DE genes. I want to draw a heatmap of these differentially expressed genes, but I h ...
ruv rna-seq heatmap written 2.1 years ago by manish200720130
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How to perform FPKM on raw reads in R
... How I perform fpkm on a file containing the raw reads of two samples and each sample have three replicates? I want to do the analysis in R. ...
R fpkm rna-seq sequencing written 2.1 years ago by manish200720130 • updated 3 months ago by Ahmed Alhendi10
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betweenLaneNormalization and calcNormFactors in RUVs
... I'm analyzing the RNAseq data using the RUVs tutorial. In this tutorial they use two functions, uq <- betweenLaneNormalization(filtered, which = "upper") s <- RUVs(uq, 1:nrow(uq), k = 2, groups) design <- model.matrix(~x + s$W) y <- DGEList(counts = filtered, group = ...
R ruvs rna-seq differential gene expression written 2.1 years ago by manish200720130

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