User: mpg33@drexel.edu

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Posts by mpg33@drexel.edu

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getSequence with biomaRt
... I am trying to DNA sequence of the upstream regulatory region of a number of genes using the biomaRt package. I start with a list of EntrezGene IDs and would like to extract the sequence from 10Kb upstream of the end of the 5'UTR to the end of the 5'UTR. I wrote a neat little package of scripts to ...
biomart written 7.6 years ago by mpg33@drexel.edu90 • updated 7.6 years ago by Marc Carlson7.2k
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Obtaining DNA sequence with biomaRt getSequence
... I am trying to DNA sequence of the upstream regulatory region of a number of genes using the biomaRt package. I start with a list of EntrezGene IDs and would like to extract the sequence from 10Kb upstream of the end of the 5'UTR to the end of the 5'UTR. I wrote a neat little package of scripts to ...
biomart written 7.6 years ago by mpg33@drexel.edu90
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globaltest mulitple testing correction
... In the paper and vignette describing the globaltest package, the authors mention the need for multiple testing when testing large numbers of pathways or functional gene groups. While I agree the number of statistical tests does need to be accounted for, I do not understand the need for additional m ...
pathways globaltest written 10.8 years ago by mpg33@drexel.edu90 • updated 10.7 years ago by Claus Mayer330
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Van de Vijver dataset probe sequences
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written 12.2 years ago by mpg33@drexel.edu90
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read.SMD ... argument
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written 12.3 years ago by mpg33@drexel.edu90 • updated 12.3 years ago by Jean Yee Hwa Yang130
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stat.diag.daB MLInterfaces
... I am new to bioconductor and classification algorithms in general. Is there a way to obtain the equation of a decision rule created when using MLInterfaces on a exprSet object? Specifically, I am using stat.diag.daB to implement DLDA. I would like to apply the same decision rule to arrays from mu ...
classification mlinterfaces written 12.7 years ago by mpg33@drexel.edu90
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Error in xval: No Direct or Inherited Method for this call
... I am tryibng to use xval to run KNNB on an exprSet object. Trying to run down the source of my difficulties I went to the xval help file and executed the example shown below (also found in the xval help file). > library(golubEsets) > data(Golub_Merge) > smallG<-Golub_Merge[200:250,] &g ...
biobase mlinterfaces written 12.8 years ago by mpg33@drexel.edu90
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xval
... I am attempting to use the xval function to run knnB on an exprSet object. The command line given by the help file doesnt seem to work. When I run lk1<- xval(smallG, 'ALL.AML', knnB, xvalMethod='LOO', group=as.integer(0)) I get the error Error in xval(smallG, "ALL.AML", knnB, xvalMethod = "LOO" ...
written 12.8 years ago by mpg33@drexel.edu90 • updated 12.8 years ago by Stephen Henderson1.0k
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SAM with censored survival data on exprSet
... I want to use significance analysis of microarrays to identify significantly altered genes selected on the basis of censored survival data. I know you can do this using the samr package, however this package does not accept data in the form of exprSets and phenoData as inputs. The sam function in ...
survival siggenes written 12.8 years ago by mpg33@drexel.edu90

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