User: vivekr

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vivekr0
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Posts by vivekr

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Getting wrong result using DESeq2
... How does DESeq2 take care of correlation in between raw counts of genes expression i.e. if two genes are positively or negatively correlated then it may affect GLM parameter estimation. Is it taken care by normalizing the counts or not? ...
written 4 days ago by vivekr0
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Comment: C: Getting wrong result using DESeq2
... Ok.Thanks for your help. ...
written 10 days ago by vivekr0
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Comment: C: Getting wrong result using DESeq2
... ok. I got it. When I try with `coef = "condition_untreated_vs_treated` then I am getting change in LFC magnitude only not sign. So according to you I should use this instead of Intercept. By changing LFC coef as untreated_vs_treated , I have got some good results but I still don't understand what ar ...
written 12 days ago by vivekr0
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Comment: C: Getting wrong result using DESeq2
... Sorry for that. I have done lfc shrinking separately from main program. That's why I forgot to attach in this question. There are two ways for shrinking. I am not sure which way to go. Here is the code : `res1 = lfcShrink(dds, coef = "Intercept", res = results(dds))` ...
written 12 days ago by vivekr0
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Comment: C: Getting wrong result using DESeq2
... I have added more information in question, please check the question again. ...
written 12 days ago by vivekr0
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Comment: C: Getting wrong result using DESeq2
... I have checked it many times. Columns of matrix are of same order them I am giving in condition. I'll check the vignette for notes on factor levels. Can you please answer the remaining questions also. An update I would like to give, in first attempt of DE analysis, hsa-mir-155 was down-regulated and ...
written 12 days ago by vivekr0
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Comment: C: Getting wrong result using DESeq2
... Thanks @Michel : Here is my command for generating cts :   cts = as.matrix(read.csv('./counts.csv', sep=", ", row.names=1)) ...
written 13 days ago by vivekr0
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Getting wrong result using DESeq2
... Hi, I am using DESeq2 for DE analysis in RNA-Seq experiment. I have 28 CLL patients raw counts and pooled male control and pooled female control raw counts. When I try to find differentially expressed miRNAs, I am getting wrong results (i.e. not matching with existing literature survey). e.g. hsa-m ...
deseq2 written 13 days ago by vivekr0
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Update package permission Everytime
... Hi,   Everytime, when I execute any of the script (NGS pipeline most of the time) in which bioconductor is called, then I got the following message every time : Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (Bio ...
rmysql software error R bioconductor written 9 months ago by vivekr0

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