User: Moshe Olshansky

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Posts by Moshe Olshansky

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Comment: C: how to combine p values?
... Thank you for references, Paul and Nikhil! --- On Fri, 10/12/10, Nikhil Garge wrote: From: Nikhil Garge Subject: Re: [BioC] how to combine p values? To: "Moshe Olshansky" , bioconductor@r-project.org, "Reema Singh" Received: Friday, 10 December, 2010, 12:25 PM There are several methods to comb ...
written 9.0 years ago by Moshe Olshansky120
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Answer: A: how to combine p values?
... Hi Reema, there are several ways to do so (you can search the Internet). I am not sure whether there exists a really good one. One possibility is as below: let P1 and P2 be the p-values from dataset 1 and dataset 2. Under the null hypothesis both p-values are distributed uniformly in [0,1]. If we a ...
written 9.0 years ago by Moshe Olshansky120
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Comment: C: RandomForest, supervised machine learning and uncertainty
... Hi January, If the situation is as you describe it, you do not need the 3rd class: stay with the two original classes and when a new case arrives, if at least 60% (or some other threshold) of votes are for class 1, make it class 1, if at least 60% (not necessarily equal to previous one) of votes ar ...
written 9.0 years ago by Moshe Olshansky120
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Answer: A: Group millions of the same DNA sequences?
... You can use the aggregate function, i.e. if X is a vector of your sequences, i.e. X[i] is a character containing your i-th sequence (i=1,2,...,100M) then do y <- aggregate(X,list(X),length) then y is a two columns data.frame with column 1 containing the sequence and column 2 containing the count. ...
written 9.1 years ago by Moshe Olshansky120
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Answer: A: method and package for imputing spectral counts from masspectrometry
... Hi Yolande, Do you mean the raw counts coming out of the instrument before any preprocessing? Regards, Moshe. --- On Tue, 26/10/10, Yolande Tra wrote: > From: Yolande Tra > Subject: [BioC] method and package for imputing spectral counts from masspectrometry > To: bioconductor at stat. ...
written 9.1 years ago by Moshe Olshansky120
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Answer: A: remove microarray batch effects using Limma
... Hi Zhi, Check whether replacing your Approach 2 by: design<-model.matrix(~0+condition.factor) exp.eset.rm.batch<-removeBatchEffect(exprs(eset),batch.factor,design) fit<-lmFit(eset.rm.batch,design) where eset.rm.batch is the expression dataset containing expression values from exp.eset. ...
written 9.1 years ago by Moshe Olshansky120 • updated 2.3 years ago by Gordon Smyth39k
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Comment: C: Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?
... Do you mean that A,B,...,E are same length and you want to apply t-test to compare (A-B)/(A-C) to D/E? Technically this is straightforward, but even if A,B,...,E are normally distributed, this is very much not true for (A-B)/(A-C) and D/E, so it won't be appropriate to apply t-test (uness A,C and E ...
written 9.3 years ago by Moshe Olshansky120
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Answer: A: Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E?
... What exactly do you mean by "equal"? --- On Tue, 24/8/10, Weibo Xie wrote: > From: Weibo Xie > Subject: [BioC] Five variables, ABCDE, how to check whether (A-B)/(A-C) is equal to D/E? > To: "Bioconductor" > Received: Tuesday, 24 August, 2010, 5:45 PM > Hello everyone, > > I ...
written 9.3 years ago by Moshe Olshansky120
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Answer: A: MAS5.0 and dChip syntax using expresso()
... Hi John, You can use mas5 instead. Alternatively, by entering mas5 you will see the code for it (including the appropriate call to expresso). Regards, Moshe. --- On Wed, 23/6/10, array chip wrote: > From: array chip > Subject: [BioC] MAS5.0 and dChip syntax using expresso() > To: bioc ...
written 9.5 years ago by Moshe Olshansky120
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Answer: A: seqinr write.fasta problem with max characters per line
... Hi Jonathan, I am not an expert on Bioconductor, however I looked at the R code for write.fasta. It uses writeLines function. This function has an argument called sep and it's default value is "\n" (newline character). This is always fine on Unix but on Windows it depends on the application: for so ...
written 9.8 years ago by Moshe Olshansky120

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