User: Lavinia Gordon

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Posts by Lavinia Gordon

<prev • 48 results • page 2 of 5 • next >
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geneplotter - buildChromLoc for arrays with no .db package
... Hi, I'd like to use the buildChromLoc function in geneplotter for GenomeWideSnp 6.0 Affymetrix arrays. As there does not appear to be a suitable .db package available for these arrays, I'm looking for any tips/pointers on how to go about this, e.g. I'm guessing one option would be to use the org.Hs. ...
go geneplotter written 5.0 years ago by Lavinia Gordon480 • updated 5.0 years ago by Marc Carlson7.2k
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Comment: C: arrayQualityMetrics and lumi - failure to load in R2.15.1 windows
... Hi Wolfgang Thank you for your message. That has resolved both issues, my apologies, I thought I had upgraded but it must have been on a different machine. Thanks for the detailed suggestions. With regards, Lavinia. Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformati ...
written 5.0 years ago by Lavinia Gordon480
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arrayQualityMetrics and lumi - failure to load in R2.15.1 windows
... Dear All, The package arrayQualityMetrics fails to load in R2.15.1: > library(arrayQualityMetrics) Error : object 'geneNames' is not exported by 'namespace:Biobase' Error: package/namespace load failed for 'arrayQualityMetrics' The library lumi also fails: > library(lumi) Loading required pa ...
lumi arrayqualitymetrics written 5.0 years ago by Lavinia Gordon480 • updated 5.0 years ago by Wolfgang Huber13k
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Comment: C: Upgrading Bioconductor using BiocUpgrade
... Thanks Dan, works perfectly, greatly appreciate your prompt response. Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformatics Murdoch Childrens Research Institute The Royal Children?s Hospital Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 www.mcri.edu.a ...
written 5.1 years ago by Lavinia Gordon480
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Upgrading Bioconductor using BiocUpgrade
... Dear all, I am trying to upgrade Bioconductor from 2.10 to 2.11 on a machine running R.2.15.0. Unfortunately this fails, unable to find function 'globalVariables'. Any advice greatly appreciated. > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.9, ?biocLite for help ...
biocinstaller written 5.1 years ago by Lavinia Gordon480 • updated 5.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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Comment: C: Translating AB/BB/AA into a SNP with Illumina data
... Hi Stephanie Thank you so much for the useful link and article. With the annotation data I have something like this: Name VALUE IlmnStrand SNP GenomeBuild Chr MapInfo 1 200006 AB TOP [A/G] 36 9 139046223 So I know AB/TOP/[A/G] means the Illumina data is reverse complem ...
written 5.3 years ago by Lavinia Gordon480
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Translating AB/BB/AA into a SNP with Illumina data
... Dear all, I am working with Illumina Human Omni1 Quad data. I only have access to processed data, e.g: ID_REF VALUE Score Theta R B Allele Freq Log R Ratio 200006 AB 0.8273118 0.4800678 2.651576 0.5337635 0.1516016 I would like to know what the SNP is at thi ...
snp crlmm written 5.3 years ago by Lavinia Gordon480 • updated 5.4 years ago by Stephanie M. Gogarten530
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Analysis of Affymetrix Cytogenetic Whole-Genome 2.7M array
... Dear all I have some data from the Affymetrix Cytogenetic Whole-Genome 2.7M array and would like to analyze it with Bioconductor. Is this possible? I wasn't able to find an appropriate annotation package and I gather that this is quite an old chip. with thanks, Lavinia Gordon. -- Senior Bioinf ...
annotation written 6.1 years ago by Lavinia Gordon480
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Comment: C: biomaRt- too many attributes selected
... Hi Steffen and Rhoda, Thank you so much for following this up. I can see that three makes sense, as I am sure that the amount of data returned can easily become enormous. It is a pity though because it is nice to know *everything* about your genes of interest! Many thanks, Lavinia. On 4/06/2011 ...
written 6.5 years ago by Lavinia Gordon480
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biomaRt- too many attributes selected
... Dear biomaRt users, Following a simple query like Task 2 in the biomaRt users guide (http://bioconductor.org/packages/2.8/bioc/vignettes/biomaRt/inst/doc/ biomaRt.pdf), getBM(attributes = myattributes, filters = "entrezgene", values = entrez,mart = ensembl) I am running into an issue with this e ...
biomart written 6.5 years ago by Lavinia Gordon480 • updated 6.5 years ago by Steffen Durinck530

Latest awards to Lavinia Gordon

Great Question 4.5 years ago, created a question with more than 5,000 views. For Upgrading Bioconductor using BiocUpgrade
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Translating AB/BB/AA into a SNP with Illumina data
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Upgrading Bioconductor using BiocUpgrade

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