User: mm2489

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mm24890
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Posts by mm2489

<prev • 17 results • page 1 of 2 • next >
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blastSequences() function in annotate package return an empty list
... Hi, I'm trying to blast a large list of short sequences (~1500 sequences, each 14 nucleotides long) using the blastSequences function from the annotate R package, and get number of hits found in the human genome + transcript DB.  The function returns a list of 0 elements even though using the web- ...
blastsequences written 2.3 years ago by mm24890 • updated 2.3 years ago by Martin Morgan ♦♦ 24k
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Using the "listValues" argument of DESEQ in multiple group comparisons
... I'm using deseq2 to find differentially expressed genes across 7 different cancer types. My goal is to obtain a list of genes differentially expressed when comparing each cancer to all others. For instance, comparing BRCA to all others. My question is about setting the "listValues" argument in the r ...
deseq2 written 2.9 years ago by mm24890 • updated 2.9 years ago by Michael Love26k
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Comment: C: problem with the dba() function in DiffBind
... Thanks Rory The peak files were re-saved as .xls separately. How can I fix this issue? ...
written 4.5 years ago by mm24890
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Comment: C: problem with the dba() function in DiffBind
... Thanks Rory I emailed the files to you. I appreciate your help ...
written 4.5 years ago by mm24890
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problem with the dba() function in DiffBind
... I'm trying to use DiffBind for re-analyses of some data. The only files that are changed from my previous run of DiffBind are the peak files from MACS2. They are still in the same format as before. Previously I was able to run Diffbind and analyse this same dataset without errors. However, now when ...
diffbind written 4.5 years ago by mm24890 • updated 4.5 years ago by Rory Stark3.0k
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Diffbind.report error too many NAs
... I'm getting the following error and I'm not sure why. Any help would be appreciated. > my.DB2 = dba.report(mydata, bCounts=TRUE) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :   solving row 1: range cannot be determined from the supplied arguments (too many NAs)   ...
diffbind written 4.6 years ago by mm24890 • updated 4.6 years ago by Rory Stark3.0k
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Comment: C: Diffbind counts vs. MACS2 scores
... Thank you so much Rory! So I ran the tests that you suggested and it looks like normalization is indeed responsible. I should mention that this chip-seq was done for a histone mark and we expect wide-spread loss of this mark in one of our experimental conditions. My main concern at this point is t ...
written 4.6 years ago by mm24890
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Comment: C: retreiving peak caller fold enrichments after generating consensus peakset in Di
... Thank you so much, this is exactly what I needed. ...
written 4.6 years ago by mm24890
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Comment: C: retreiving peak caller fold enrichments after generating consensus peakset in Di
... Yes, I understand the difference. The peak caller score has to do with peaks being real or not compared with the input control, whereas the peak scores generated by dba.count have to do with intensity of each peak/number of reads mapping to each peak. I was hoping I can still get some score equival ...
written 4.6 years ago by mm24890
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Comment: C: retreiving peak caller fold enrichments after generating consensus peakset in Di
... Thank you both for your help. I guess the problem is that I want peak caller scores but only for the consensus peaks, which means only the peak set generated after I call dba.count(), right? ...
written 4.6 years ago by mm24890

Latest awards to mm2489

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Exporting dba.count result as a data frame
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Exporting dba.count result as a data frame
Popular Question 2.8 years ago, created a question with more than 1,000 views. For problem with the dba() function in DiffBind
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Diffbind counts vs. MACS2 scores

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