User: igor

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igor10
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Posts by igor

<prev • 59 results • page 1 of 6 • next >
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Comment: C: DiffBind matrix of values
... I am using DESeq2-based analysis, so thanks for clarifying that part. I guess DBA_SCORE_RPKM should be close enough (or as close as possible) for something like plotting. Is there a chance DESeq2 normalization becomes an option at some point? If you are just using plain DESeq2, they provide an opti ...
written 7 months ago by igor10
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DiffBind matrix of values
... I am using DiffBind and trying to export the matrix of values for all peaks. If I use dba.report() with bcounts=TRUE, I get those values, but it's only for the two groups being compared. What if you have more than two groups? I tried dba.peakset() with bRetrieve=TRUE. That seems to return what I wa ...
diffbind written 7 months ago by igor10 • updated 7 months ago by Rory Stark1.7k
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DiffBind for ATAC-seq
... Normally, DiffBind is used for ChIP-seq data, but I've seen it used for ATAC-seq as well. I don't see any issues with that. MACS can be used for the initial peak calling. However, when performing peak calling for ATAC-seq data, it is advised to adjust the default parameters so peaks are centered on ...
diffbind peak finding macs atac-seq macs2 written 7 months ago by igor10 • updated 5 weeks ago by kennethcondon200710
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DESeq2 counts distribution across both genes and samples
... DESeq2 assumes negative binomial distribution for counts distribution. That refers to the distribution of counts for a single gene across all samples. What about distribution of counts of all genes across one sample? Each sample is normalized based on the geometric mean of all counts (or size facto ...
rnaseq deseq2 written 7 months ago by igor10 • updated 7 months ago by Michael Love11k
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using variable in design formula
... Many packages that do statistical analysis (such as DESeq2 or DEXSeq), use a design formula to specify the exact comparison. For example: DESeqDataSet(se, design = ~ condition) Where "condition" is the actual column name. I'd like to have the column name be adjustable. I tried using a variable in ...
deseq2 R design matrix written 8 months ago by igor10 • updated 8 months ago by Michael Love11k
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DiffBind "no lines available in input" error
... Sometimes my ChIP-seq samples do not get any significant peaks by MACS, so the output peaks file is empty. When I use that file in DiffBind sample sheet, I get an error: Error in read.table(fn, blank.lines.skip = T, header = T) : no lines available in input Calls: dba ... pv.peakset -> pv.re ...
chipseq diffbind written 9 months ago by igor10 • updated 9 months ago by Rory Stark1.7k
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ChIPseeker gene body plot
... ChIPseeker has plotAvgProf() that will make a profile plot of a certain distance from a single point. Is there something similar for gene body profiles? It's a similar idea, but instead of a single point, it's a variable length region in the middle, so you have to normalize for length. Here is an e ...
visualization chipseeker written 10 months ago by igor10 • updated 10 months ago by Guangchuang Yu630
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Comment: C: Bioconductor HTML docs seem to be broken
... Thank you! I don't know if it was supposed to have an HTML vignette. I just noticed that for every package I tried, it was broken. I wanted to use something popular as an example. ...
written 11 months ago by igor10
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Answer: A: nice 3D displays for PCA analysis
... Here is a nice tutorial: http://planspace.org/2013/02/03/pca-3d-visualization-and-clustering-in-r/ Or even here in Bioconductor support: https://support.bioconductor.org/p/53559/   ...
written 11 months ago by igor10
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Bioconductor HTML docs seem to be broken
... For the last few days, the links to HTML docs for all packages seem to be broken. For example, on https://bioconductor.org/packages/release/bioc/html/DESeq2.html the HTML link points to https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/doc and that page does not exist. PDF and ...
bioconductor written 11 months ago by igor10

Latest awards to igor

Popular Question 13 days ago, created a question with more than 1,000 views. For minfi MethylationEPIC errors
Supporter 15 months ago, voted at least 25 times.

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