User: jivarajivaraj

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Posts by jivarajivaraj

<prev • 33 results • page 1 of 4 • next >
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Estimating sample size for specific platforms
... Hi, I want to estimate sample size for a specific RNA-seq platform named HTG EdgeSeq in which 2500 cancer related genes being profiled; I have used RnaSeqSampleSize package but process never finished > sample_size(power = 0.8, m = 2500, m1 = 200, f = 0.1, k = 1, w = 1, + rho ...
software error R rna-seq rnaseqsamplesize written 4 weeks ago by jivarajivaraj10
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Comment: C: Appropriate experimental design for differential expresion
... Sorry @Aaron Lun, I seriously have been asked to suggest an expermental design for this RNA-seq for which the ultimate goal is identifying genes coming from the interaction of fibroblast cells and organoid cells. Then how would be a reasonable design please? Thanks a lot in advance ...
written 8 weeks ago by jivarajivaraj10
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Comment: C: Appropriate experimental design for differential expresion
... Sorry @Aaron Lun, I seriously have been asked to suggest an expermental design for this RNA-seq for which the ultimate goal is identifying genes coming from the interaction of fibroblast cells and organoid cells. Then how would be a reasonable design please? Thanks a lot in advance ...
written 8 weeks ago by jivarajivaraj10
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Comment: C: Appropriate experimental design for differential expresion
... Sorry I am likely a beginner in computational biology in our lab. The other postdoc is planning the experiment and has not done anything yet. My job is guiding her not to spend a lot of money on none sense things. She wants to recognize differentially expressed genes due to the co-culturing of fibro ...
written 8 weeks ago by jivarajivaraj10
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Appropriate experimental design for differential expresion
... Hi, Sorry I am designing an RNA-seq experiment so I need help to be wise enough before invest any money; could I please ask you if the design gives what I want? You please imagine I have 1- 3 replications of fibroblast surrounding a tumor, 2- an 3 replications organoid (3D model) of this tumor and ...
normalization cancer edger written 8 weeks ago by jivarajivaraj10 • updated 8 weeks ago by swbarnes2170
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Problem in installing
... Hi, I don't know how to solve this error in installing DESeq2 Any help please? > library(DESeq2) Loading required package: GenomicRanges Error: package ‘S4Vectors’ 0.18.1 is loaded, but >= 0.19.11 is required by ‘GenomicRanges’ In addition: Warning message: package ‘DESe ...
deseq2 software error written 8 weeks ago by jivarajivaraj10 • updated 8 weeks ago by Martin Morgan ♦♦ 23k
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Getting a signature specific to each patient
... Hi, I have 6 RNA-seq samples like this 4 patients (005, 036, 121, 013) I have 3 tumour samples and 3 cancer models (organoid) This is PCA of log transformed data by DESeq2 (tumour Vs. organoid) [![enter image description here][1]][1] [1]: https://i.stack.imgur.com/n7fID.jpg In ...
cancer deseq2 R written 11 weeks ago by jivarajivaraj10 • updated 11 weeks ago by James W. MacDonald50k
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Is DESeq2 performs the same when I am loading library DESeq2?
... Hi, HTG EdgeSeq assay provides a toolkit doing differential expression by DESeq2. I compared results coming by this software and when I am doing DESeq2 in R version 3.5.1 manually like dds=DESeqDataSetFromMatrix(countData = df, colData = mycols, design = ~ condition) dds <- DESeq( ...
deseq2 written 3 months ago by jivarajivaraj10 • updated 3 months ago by Michael Love23k
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Comment: C: edgeR or wilcoxon rank test? Which is right?
... Sorry, I just edited my post. I have used cpm log values for any t-test or non-parametric test ...
written 3 months ago by jivarajivaraj10
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Comment: C: edgeR or wilcoxon rank test? Which is right?
... Thanks a lot, this is edgeseq a sort of RNAseq that does not need RNA extraction. However I fed cpm normalized data after log by cpm function in edgeR into wilcoxon test and same group for edgeR. Is wilcoxon not wrong yet even with normalized read counts? I saw people use mann withney for such dat ...
written 3 months ago by jivarajivaraj10

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