User: igor

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igor20
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Posts by igor

<prev • 63 results • page 1 of 7 • next >
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Counting exonic reads with DEXSeq and GenomicAlignments
... The DEXSeq vignette describes several protocols for obtaining exon counts. One option is to use the dexseq_count.py script (powered by htseq) that comes with the package. Another option is to use summarizeOverlaps directly in R. I tried both methods with unstranded parameters and the results were id ...
dexseq genomicalignments exon usage written 6 weeks ago by igor20
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Comment: C: DESeq: large difference in number of replicates per condition
... I would add that you should also pay attention to outlier filtering/replacement (see DESeq minReplicatesForReplace) if you expect your large group to be heterogenous. I've seen people run into trouble with that when handling large groups. ...
written 6 weeks ago by igor20
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Comment: C: How to normalize Microarray expression data?
... Although the question says "Affymetrix SNP 6.0 data", it also says "Microarray expression Data". Thus, it may very well be an expression array, not a SNP array. Then gene symbols would make sense. ...
written 6 weeks ago by igor20
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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 5 months ago by igor20
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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 14 months ago by igor20
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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 14 months ago by igor20 • updated 14 months ago by Rory Stark2.1k
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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 14 months ago by igor20 • updated 8 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 14 months ago by igor20 • updated 14 months ago by Michael Love14k
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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 15 months ago by igor20 • updated 15 months ago by Michael Love14k
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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 16 months ago by igor20 • updated 16 months ago by Rory Stark2.1k

Latest awards to igor

Popular Question 5 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 6 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 7 months ago, created a question with more than 1,000 views. For minfi MethylationEPIC errors
Supporter 22 months ago, voted at least 25 times.

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