User: r.chereji

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r.chereji0
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Posts by r.chereji

<prev • 5 results • page 1 of 1 • next >
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Answer: A: cummeRbund sigMatrix wrong counts
... I noticed the same problem: the number of DEGs reported by sigMatrix is higher than the numbers reported by getSig using the same alpha. I would appreciate if someone could clarify why these 2 functions report different numbers and how one could use these 2 functions to get identical results. Here ...
written 21 months ago by r.chereji0
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Comment: C: How to reproduce the PCA plot from DiffBind
... Hi Rory,   Thanks for the link, but some of the counts given by "counts = dba.peakset(tamoxifen, bRetrieve=TRUE)" are "-1" so I can't take logarithm of that... Can you please check once more my example and tell me what is done differently by DiffBind? Thanks, Razvan   ...
written 2.5 years ago by r.chereji0
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How to reproduce the PCA plot from DiffBind
... Hi, I'm trying to understand what exactly is done by the dba.plotPCA function from DiffBind. I tried to reconstruct the plot generated by dba.plotPCA but for some reason I get a different plot. Could you please check what I tested and tell me what is done differently by the dba.plotPCA function? T ...
diffbind written 2.5 years ago by r.chereji0 • updated 2.5 years ago by Rory Stark2.5k
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Comment: C: DiffBind: correlation heat map
... Thanks Rory! That is useful, but I had something else in mind. Suppose I have 6 samples: A_treated, A_untreated, B_t, B_u, C_t, C_u. By default dba.plotHeatmap will generate a 6x6 correlation heatmap with the correlations among all 6 samples. I would like to generate a correlation heatmap among the ...
written 2.5 years ago by r.chereji0
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DiffBind: correlation heat map
... Hi, I used DiffBind to count the ChIP-seq reads (dba.count) and plot the correlation heat map (dba.plotHeatmap), and a have a question. By default dba.plotHeatmap uses all the samples and computes the correlations between every pair, and I would like to compute and plot the correlations only among ...
diffbind written 2.5 years ago by r.chereji0 • updated 2.5 years ago by Rory Stark2.5k

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