User: Sameet Mehta

gravatar for Sameet Mehta
Sameet Mehta20
Reputation:
20
Status:
New User
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
3 months, 2 weeks ago
Joined:
9 years, 11 months ago
Email:
m******@gmail.com

Posts by Sameet Mehta

<prev • 12 results • page 1 of 2 • next >
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Comment: C: readCufflinks problem with extdata
... This does not seem to work always.  I kept getting error about `Gviz`, and `cummeRbund` not being compatible with `RSQLite` version `1.1-2`.  It worked on my Laptop, but cannot get it to work on the cluster. ...
written 3 months ago by Sameet Mehta20
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Answer: A: Error in installing Gviz
... It seems the easiest fix is biocValid(fix = T). ...
written 6 months ago by Sameet Mehta20
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Comment: C: How to use diffHiC with existing contact matrices?
... Understood. ...
written 11 months ago by Sameet Mehta20
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Comment: C: How to use diffHiC with existing contact matrices?
... Hi @Aaron, I have managed to reach this point.  In the `diffHic` User manual, I am reading chapter 7.  But I do not see how/where to plug in the `data` generated above. ...
written 11 months ago by Sameet Mehta20
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Comment: C: How to use diffHiC with existing contact matrices?
... Sorry, wt.df is the sparse matrix that holds the interaction strength (raw counts). > head(wt.df) bin1 bin2 strength 1: 40 99 1 2: 41 100 1 3: 65 279 1 4: 71 285 1 5: 285 299 1 6: 299 305 1 bin.gr is the GRanges object that holds t ...
written 11 months ago by Sameet Mehta20
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Comment: C: How to use diffHiC with existing contact matrices?
... The interaction matrix with count data is in sparse format.  Will that still work?  I get the following error:      wt.1 <- ContactMatrix(as.matrix(wt.df), bin.gr, bin.gr)     Error in validObject(.Object) :       invalid class “ContactMatrix” object: 'matrix' nrow must be equal to length of 'a ...
written 11 months ago by Sameet Mehta20
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Answer: A: How to use diffHiC with existing contact matrices?
... Hi @Aaron, thank you.  This is useful.  Can you give me an idea of what columns should be in the `GRanges` object.  I do have raw matrices generated as part of the pipeline.  The `bin` information is as follows:     chr1    0    2500    1     chr1    2500    5000    2 Is this information enough?   ...
written 11 months ago by Sameet Mehta20
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How to use diffHiC with existing contact matrices?
... Currently I am in the process of analyzing HiC data from two different conditions.  When I talked to some colleagues about best way of analyzing and comparing two HiC data-sets, I was asked to look at the `diffHiC`.   I read the user-manual and the paper.  Congratulations on the paper.  I have a que ...
diffhic hicpro written 11 months ago by Sameet Mehta20
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Comment: C: Cannot re-create q-values from the p-values in the DiffTable.
... To the best of my understanding, the `q_value`s are calculated based on the `p_value`s.  So if i have a vector of p-values, `q_value <- p.adjust(p_value, method = "BH")`, as given in the cummeRbund source code should hold even if I just use the p-values column from the diffData output.  Why does ...
written 22 months ago by Sameet Mehta20
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Cannot re-create q-values from the p-values in the DiffTable.
... Hi, I read on the SeqAnswers forum that the q_value in CuffDiff, is basically p.adjust(pvalue, method = "BH").  However, when I take the p_value column from a diffData(x, c1, c2), and try to use p.adjust(p_value, method = "BH"), I do not get the same q_values back.  Am I doing anything wrong? ...
qvalue cummerbund adjusted pvalue pvalue written 22 months ago by Sameet Mehta20 • updated 22 months ago by James W. MacDonald45k

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