User: Udi Landau

gravatar for Udi Landau
Udi Landau30
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2 years, 9 months ago
Email:
u*********@mail.huji.ac.il

Posts by Udi Landau

<prev • 11 results • page 1 of 2 • next >
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Comment: C: why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM
... From what I know the fold change of edgeR and DESeq2 is calculated using normalization other than fpkm. I would use one of edgeR or DESeq2. ...
written 11 weeks ago by Udi Landau30
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Comment: C: use only lib size as normalizing factor in edgeR
... Thank you! Can you tell me what would you recommend to use for plotting the data? I understand that the pseudo count is not suitable?  ...
written 11 weeks ago by Udi Landau30
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use only lib size as normalizing factor in edgeR
... Hello,  I would like to use only the lib size as normalizing factor in edgeR, so I am doing this: cds <- DGEList(counts = counts, group = group, norm.factors = MyNormFactors) I skip the  cds <- calcNormFactors(cds, method = "none") Because It will bring the norm factor back to 1.. and ...
edger written 11 weeks ago by Udi Landau30 • updated 11 weeks ago by Aaron Lun21k
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Comment: C: How to get peaks summit using dba.peakset
... Thank you for your quick reply!  I see that I get the summits for each replicate. How can I get the summit of the consensus peaks?. I tried to add the argument 'consensus = -DBA_REPLICATE' to the dba.peakset command but it didn't change the output.  When I think of it.. is there one peak that re ...
written 3 months ago by Udi Landau30
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How to get peaks summit using dba.peakset
... Hi, I cannot find the way to get the coordination for the summits of my peaks. I added the summit option to the dba.count and I am looking at the dba.peakset documentation and cannot figure out how to get the data.. Is there a way to get the summits of the peaks together with the differential aff ...
diffbind written 3 months ago by Udi Landau30 • updated 3 months ago by Rory Stark2.6k
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Annotation missing when using makeTxDbFromGFF
... Hi, I am using the instructions from here  to make a GRange object form my TxDb. I don't see annotation that is in my GFF file (transposable element) and also the numbers of some of the feature are different from those I get using grep on the GFF file. Any ideas how can I fix that? Thank you ...
maketxdbfromgff written 2.8 years ago by Udi Landau30
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Comment: C: How to use DiffBind to get consensus peaks I am interested in?
... Look here https://support.bioconductor.org/p/67306/#67309 ...
written 2.8 years ago by Udi Landau30
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Comment: C: question about correlation plots generated by Diffbind based on peak occupancy
... You can get the peak scores from MACS2 NAME_peaks.narrowPeak file.. # I write it as an answer by mistake.. ...
written 2.8 years ago by Udi Landau30
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Answer: A: question about correlation plots generated by Diffbind based on peak occupancy
... You can get the peak scores from MACS2 NAME_peaks.narrowPeak file ...
written 2.8 years ago by Udi Landau30
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Comment: C: same numbers in dba.overlap
... Thanks Valerie.  ...
written 2.8 years ago by Udi Landau30

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