User: Straubhaar, Juerg

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Posts by Straubhaar, Juerg

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Comment: C: svg error in arrayQualityMetrics
... Hi Wolfgang, My cairo version is 1.12.14 and I didn't like to update to your version since for gentoo linux version 1.12.16 is still unstable. But I used arrayQualityMetrics devel version and it worked with cairo version 1.12.14. I apologize for bothering you. I should have thought about testing ...
written 5.6 years ago by Straubhaar, Juerg300
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svg error in arrayQualityMetrics
... I am running the arrayQualityMetrics with: arrayQualityMetrics(expressionset=esett,outdir="TestAQM",force=TRUE,do .logtransform=FALSE,intgroup="SomeCategory") and get the following errror: Error in tmp[i] : invalid subscript type 'list' The error is generated in a 'brittle' part of the arrayQual ...
go arrayqualitymetrics written 5.6 years ago by Straubhaar, Juerg300 • updated 5.6 years ago by Andrzej Oleś720
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Answer: A: SOM clustering
... I used this code, taken from http://manuals.bioinformatics.ucr.edu/hom e/R_BioCondManual#R_clustering, the very helpful, for all kinds of things, manuals by T. Gierke at University of California Riverside. library(som) # Loads the required SOM library. y <- matrix(rnorm(50), 10, 5, dimnames=list ...
written 7.7 years ago by Straubhaar, Juerg300
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beadarray error
... Hi, The code snippet in analyseDirectory: storemet<-NULL for(i in fmet){ storemet <- rbind(storemet,read.table(file.path(dir,fileList[i],fsep = .Platform$file.sep),header=T,as.is=T,sep="\t")) fileList <- fileList[-i]; } produces the error: Error in rbind(depars ...
written 8.2 years ago by Straubhaar, Juerg300
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Comment: C: connecting to ensembl
... Hi Herve, code: library(biomaRt) mart <- useMart("ensembl","rnorvegicus_gene_ensembl") attr.g <- c("rgd_symbol","ensembl_gene_id","chromosome_name","start_position", "end_position","strand") ensGene <- getBM(attributes=attr.g,mart=mart) I run the code on the commandline R ...
written 8.4 years ago by Straubhaar, Juerg300
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biomaRt error
... Running example(getSequence) returns an error. See below. Juerg, UMass Med School > library(biomaRt) > example(getSequence) gtSqnc> if(interactive()){ gtSqnc+ mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") gtSqnc+ gtSqnc+ seq = getSequence(id="BRCA1", type="hgnc_symbol", ...
written 10.5 years ago by Straubhaar, Juerg300 • updated 10.5 years ago by Rhoda Kinsella660
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Is retrieving exon sequences with biomaRt a random process?
... I am using the following code to retrieve the exon sequences of gene Tcfap2b with GeneID:21419. There are 8 exons for this gene. for (i in sequence(50)) { + x <- getSequence(id=21419,type="entrezgene",seqType="gene_exon",mart =ensembl) + if (is.null(x)) print('NULL result') + if (!is.null(x)) p ...
written 10.5 years ago by Straubhaar, Juerg300 • updated 10.5 years ago by Wolfgang Huber13k
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namespace error with goProfiles package
... The following code is from the goProfiles package and works fine: require(goProfiles) data(prostateIds) welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") ...
go mouse4302 goprofiles written 11.4 years ago by Straubhaar, Juerg300 • updated 11.4 years ago by Alex Sanchez20
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FW: Error using ABarray
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080228/ 954ccefe/attachment.pl ...
written 11.6 years ago by Straubhaar, Juerg300
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Answer: A: Rat Nimblegen promoter dataset HOWTO
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080117/ ff7003b9/attachment.pl ...
written 11.8 years ago by Straubhaar, Juerg300

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