User: Anne Deslattes Mays

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United States
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4 weeks ago
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4 years, 5 months ago
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Posts by Anne Deslattes Mays

<prev • 5 results • page 1 of 1 • next >
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Comment: A: limma results versus topTable
... Okay -- I am wrong the rownames are in fact preserved.  However, I still do not get what I want -- what I want is to have the rows that are most significantly over and under expressed -- the results gives the breakdown, but they are not sorted by p-value -- so I imagine I can do this.   But advice a ...
written 28 days ago by Anne Deslattes Mays10
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limma results versus topTable
... Hello, I'm trying to create a reduced matrix after running lmFit, contrasts.fit and eBayes from limma.   To do so, ideally the rownames of the results match the rownames of the original matrix. For example, this is the case with topTable: >CasevsCtrl.top100 = topTable(iefit,coef=1,n=100,sort= ...
limma written 28 days ago by Anne Deslattes Mays10 • updated 26 days ago by Gordon Smyth32k
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edgeR:processAmplicons barcode match only 57% when it should be 100% -- I artificially inserted them -- are there other assumptions
... Hi There, I inserted all my barcodes myself into the fastq files -- they should have matched 100% -- but they did not.  Based upon a previous thread regarding the processAmplicons runtime when you allow for mismatches, I turned mismatching basically off just so I could see a return.   I have 2 pair ...
edger processamplicons shrna written 2.1 years ago by Anne Deslattes Mays10 • updated 24 months ago by thomas.leete0
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Comment: C: edgeR: processAmplicons crashes with large number of hairpins
... Okay -- since my run of 200k shRNAs and only 4-5 million reads is taking > 2 hours I went back and read the above thread -- it appears I should run this with allowMismatch=False.   I can imagine we could speed this up if we could parallelize the tasks -- if there is an internal qsort like step -- ...
written 2.1 years ago by Anne Deslattes Mays10
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Answer: A: Error loading GO.db
... Hi Dan, I do as you say and still get the error.... Would that I could unlink the two :-<. I am on a Mac book Pro -- OSX 10.8.3, Error : .onLoad failed in loadNamespace() for 'GO.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not fo ...
written 4.5 years ago by Anne Deslattes Mays10

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