User: jivarajivaraj

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Posts by jivarajivaraj

<prev • 28 results • page 1 of 3 • next >
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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 3 days ago by jivarajivaraj10 • updated 3 days 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 20 days ago by jivarajivaraj10 • updated 20 days ago by James W. MacDonald49k
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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 6 weeks ago by jivarajivaraj10 • updated 6 weeks ago by Michael Love22k
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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 7 weeks 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 7 weeks ago by jivarajivaraj10
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edgeR or wilcoxon rank test? Which is right?
... Hi, I have histopathologic response to neoadjuvant chemoradiation in 56 cancer samples. A total of 26 samples were classified as minor and 30 as major histopathologic responders (TRG1-2 and TRG4-5 respectively). I have done edgeR and wilcoxon test to find genes driving the difference of tumor sampl ...
cancer edger R rna-seq wilcox written 7 weeks ago by jivarajivaraj10
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Comment: C: Batch correction for a sets of genes
... Thank you, they are Oncology Biomarker Panel and Precision Immuno-oncology Panel in HTG assay ...
written 8 weeks ago by jivarajivaraj10
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Batch correction for a sets of genes
... Hi, I have **2545** and **1402** genes in **Oncology Biomarker Panel** and **Precision Immuno-oncology Panel** respectively. I have **719** common genes between two panels. I will need to merge raw read counts from these panels for differential expression (we know experimental condition, chemistry ...
rnaseq cancer deseq2 R written 8 weeks ago by jivarajivaraj10 • updated 8 weeks ago by Michael Love22k
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Comment: C: How can I use DESeq2 for exploratory analysis after batch effect removal using R
... Sorry, I have such design condition batch A1 treatment 1 A2 treatment 1 A3 treatment 1 A4 treatment 1 A5 treatment 1 A6 treatment 1 A7 control 1 A8 control 1 A9 control 1 A10 control 1 A11 control 1 A12 control 1 B1 treatment ...
written 8 weeks ago by jivarajivaraj10
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Comment: C: Different results with DESeq2 and EdgeR
... Thanks a lot, very helpful. Sorry as I mentioned already this is not a RNA-seq rather HTG EdgeSeq only targeting 2560 oncology biomarkers. Do you think could I use DESeq2 or edgeR for differential expression or should I use t-test (the distribution of reads is not normal though)? I saw a post menti ...
written 8 weeks ago by jivarajivaraj10

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