User: vivekr

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vivekr0
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Posts by vivekr

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Is Background Correction necessary before DESeq analysis
... Thanks Michal for your response. As we know that small RNA-seq counts data is very heterogeneous. So, it is highly possible to have some miRNAs with poor counts and some miRNAs with very high counts. If majority of counts data is either sparse or have poor counts then its different. In my case, I fo ...
written 4 weeks ago by vivekr0
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Is Background Correction necessary before DESeq analysis
... Hi, I am working on small RNA-seq data and want to identify differentially expressed miRNAs. I know how to do it with DESeq2 and I have got 8 miRNAs as differentially expressed. But I have seen that some authors also do background correction (BC) before applying DESeq2 on raw count data. Background ...
cancer deseq2 written 5 weeks ago by vivekr0 • updated 5 weeks ago by Michael Love24k
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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 5 months ago by vivekr0
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Comment: C: Getting wrong result using DESeq2
... Ok.Thanks for your help. ...
written 5 months 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 5 months 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 5 months 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 5 months 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 5 months 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 5 months 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 5 months ago by vivekr0

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