User: Scott Ochsner

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Scott Ochsner300
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Posts by Scott Ochsner

<prev • 30 results • page 1 of 3 • next >
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Answer: A: mget plus regular expression
... Marco, With your query you have asked for the hgug4112a array features mapped to refseq NM_016951. There are apparently three. Scott Scott A. Ochsner NURSA Bioinformatics Resource Baylor College of Medicine -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:biocond ...
written 8.9 years ago by Scott Ochsner300
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Answer: A: finding and deleting repeated observations
... Hi Mervi, One solution is to order your data frame by "pvalue" using the order function and then to remove duplicate "GeneSymbol" using !duplicated. > A<-c(12,2,4,15,11,9) > B<-c(44,32,55,25,27,18) > pvalue<-c(.01,.05,.2,.005,.002,.0001) > GeneSymbol<-c(rep("ABC1",2),"AB",r ...
written 9.1 years ago by Scott Ochsner300
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forcePositive background option from lumiB
... Hi, I'm interested in finding out just how the forcePositive background correction is implemented. The lumiB help file description of the offset (minus minimum value plus one) is a little vague for me to grasp. Could someone please point me to a reference or code which I can use to understand how ...
written 9.7 years ago by Scott Ochsner300
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Comment: C: "topGOdata" object: How to supply gene scores with a predefined list of genes
... Hi Adrian, Thanks for the response. You have confirmed for me that at the moment it is not possible to create a geneSel function which utilizes more than one argument. Unfortunately, I want to utilize a fold change cutoff in addition to a p.value cutoff. The only way I can do this is to ...
written 9.8 years ago by Scott Ochsner300
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"topGOdata" object: How to supply gene scores with a predefined list of genes
... Hi, I would like to attach gene "score" info to a predefined list of interesting genes to generate a topGOdata object. The predefined list of genes was obtained by: > library(limma) > library(topGO) > input<-cbind(FC=fit$coefficients[,1],pval=p.adjust(fit$p.value[,1],met ho d="BH")) &g ...
go written 9.8 years ago by Scott Ochsner300 • updated 9.8 years ago by Adrian Alexa400
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Answer: A: venn diagram
... Steve, Subtract the list of genes bounded by circles from the total. You should be able to build a list of probeids bounded by circles with: >within<-c(alls.genes[[1]], alls.genes[[2]], alls.genes[[4]], etc...) #subtract these from the input by: >outside<-setdiff(rownames(temp.resul ...
written 9.9 years ago by Scott Ochsner300
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Answer: A: venn diagram
... Steve, I don't remember exactly where I picked this bit of code up so I apologize for not giving credit. I'm almost sure I got it from looking at the mail archives. It uses the makeIndices function within affycoretools. >vennDiagram(temp.results) # make an index of all the probeIds with a TR ...
written 9.9 years ago by Scott Ochsner300
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duplicateCorrelation question
... Dear list, I have an array with duplicate spots that are not evenly spaced. The help for duplicateCorrelation indicates that the spots should be spaced evenly and designated using the spacing argument. I'm wondering if I can order the rows of my MAlist such that the duplicate spots are on evenly ...
written 10.5 years ago by Scott Ochsner300
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Comment: C: Help with loading newly created custom annotation db into R session
... Dear list, I'm following up with my install progress to complete this thread. After following the directions from the R Installation and Administration manual I downloaded Rtools minus the cygwin .dlls and edited my path to look as below: PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGw\bin;C ...
written 10.5 years ago by Scott Ochsner300
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Help with loading newly created custom annotation db into R session
... Dear list, How do I load a custom annotation package into an R session? I've created a custom annotation database by following the steps laid out in the SQLForge vignette using the gui version of R with windows XP. Up until now, all I've had to do to load an annotation package into an R session is ...
annotation go gui zebrafish probe written 10.5 years ago by Scott Ochsner300 • updated 10.5 years ago by James W. MacDonald50k

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