User: igor

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igor10
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Posts by igor

<prev • 60 results • page 1 of 6 • next >
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minfi estimateCellCounts normalized beta values adjusted for cell type
... There is an estimateCellCounts() function in minfi. One of the parameters is returnAll which returns normalized user supplied data. That is returning quantile-normalized values that were normalized along with the reference dataset. Is there a way to get values adjusted by cell-type composition? The ...
minfi 450k written 3 months ago by igor10
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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 12 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 12 months ago by igor10 • updated 12 months ago by Rory Stark2.0k
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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 13 months ago by igor10 • updated 6 months 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 13 months ago by igor10 • updated 13 months ago by Michael Love13k
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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 13 months ago by igor10 • updated 13 months ago by Michael Love13k
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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 14 months ago by igor10 • updated 14 months ago by Rory Stark2.0k
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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 15 months ago by igor10 • updated 15 months ago by Guangchuang Yu700
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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 16 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 16 months ago by igor10

Latest awards to igor

Popular Question 3 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 4 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 5 months ago, created a question with more than 1,000 views. For minfi MethylationEPIC errors
Supporter 20 months ago, voted at least 25 times.

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