User: bioinfouser

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bioinfouser70
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Posts by bioinfouser

<prev • 46 results • page 2 of 5 • next >
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Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
... Thank you! I will look into it more! ...
written 7 weeks ago by bioinfouser70
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Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
... Thank you very much! That's very helpful! ...
written 7 weeks ago by bioinfouser70
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How to avoid hardcoding in R? How to automatize R scripts?
... Hello, This is not directly related to any particular analysis. I have been doing my own analysis for rna seq data for the last one year, completely learning from here and there. Until now, I am confident and can do my own analysis. I always use Rstudio to write and run the scripts for my data anal ...
R chip-seq r programming rna-seq written 7 weeks ago by bioinfouser70
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... Dear Rory, Thank you very much for your swift reply! I understand now completely! I will do my analysis accordingly. One last question regarding normalisation, if I use `DESeq2` normalization for ChIPseq analysis, would it equal to `DiffBind` simple normalisation in terms of the results? Also, I ...
written 8 weeks ago by bioinfouser70
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... I will go through the link. Thanks! ...
written 8 weeks ago by bioinfouser70
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... I see. I might be wrong then! But this is mentioned in the DESeq2 vignette: > The DESeq2 model internally corrects for library size, so transformed or normalized values such as counts scaled by library size should not be used as input. ...
written 8 weeks ago by bioinfouser70
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Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
... Thanks a lot for responding so quickly! Could you please elaborate on the library size normalisation question that I had? Say, in DESeq2, the library is the colSums of raw counts. But DiffBind uses probably total mapped reads from the bam file. These are fundamentally different library sizes. Then, ...
written 8 weeks ago by bioinfouser70
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Difference of DiffBind library size normalisation vs DESeq2 library size normalisation
... For ChIPseq analysis, I was using DiffBind until now but want to switch to deseq2 as I want to control for multiple covariates, which is not currently offered by DiffBind package AFAIK(only one blocking factor at a time, even though I concatenate the blocking factors). I have the raw counts generate ...
diffbind deseq2 chip-seq rna-seq normalisation written 8 weeks ago by bioinfouser70 • updated 8 weeks ago by Rory Stark670
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Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
... Dear kevin, one small question. Does your package "pcatools" allow taking the deseq2 object directly to make pca plots? Or one needs to some steps? I find your package fascinating and want to use it, that's why wondering. ...
written 8 weeks ago by bioinfouser70
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Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
... Thank you, Kevin! I immensely appreciate your detailed explanation! Also, I found in the Vignette: > **Do normalized counts correct for variables in the design?** No. The design variables are not used when estimating the size factors, and counts(dds, normalized=TRUE) is providing counts scaled ...
written 8 weeks ago by bioinfouser70

Latest awards to bioinfouser

Popular Question 8 weeks ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r
Supporter 9 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r
Popular Question 22 months ago, created a question with more than 1,000 views. For mm10 enhancer annotation for ngs.plot.r

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