## User: Sameet Mehta

Sameet Mehta30
Reputation:
30
Status:
New User
Location:
United States
Scholar ID:
Last seen:
1 year, 1 month ago
Joined:
10 years, 9 months ago
Email:
m******@gmail.com

#### Posts by Sameet Mehta

<prev • 12 results • page 1 of 2 • next >
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... 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 13 months ago by Sameet Mehta30
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Answer: A: Error in installing Gviz
... It seems the easiest fix is biocValid(fix = T). ...
written 16 months ago by Sameet Mehta30
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... Understood. ...
written 21 months ago by Sameet Mehta30
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... 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 21 months ago by Sameet Mehta30
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... 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 21 months ago by Sameet Mehta30
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... 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 21 months ago by Sameet Mehta30
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... 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 21 months ago by Sameet Mehta30
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... 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 ...
written 21 months ago by Sameet Mehta30
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... To the best of my understanding, the q_values are calculated based on the p_values.  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 2.7 years ago by Sameet Mehta30
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... 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? ...
written 2.7 years ago by Sameet Mehta30 • updated 2.7 years ago by James W. MacDonald47k

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