User: Lavinia Gordon

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Posts by Lavinia Gordon

<prev • 48 results • page 1 of 5 • next >
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RTPCR - concentration rather than Ct
... Dear all, I have some rtpcr data where the control genes show considerable differences in Ct values at their two locations (at the start and at the end of the plate). I've used HTqPCR in the past (thanks Heidi!) with great results. However in this case I am working with the concentrations (calcul ...
htqpcr written 4.5 years ago by Lavinia Gordon480
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Statistical Genetics Post-doc position available in Melbourne
... Post-doc, Statistical Genetics Murdoch Childrens Research Institute For further information about the position please contact Dr Stephen Leslie (email: stephen.leslie at mcri.edu.au or telephone: +61 3 9345 7042). Please note that excellent candidates with a strong statistical background from any ...
genetics written 4.5 years ago by Lavinia Gordon480
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Comment: C: methyAnalysis - changes to GenoSet
... Argh!, thanks Martin, sorry about that. So in that case I think I've worked out a (rather ugly) way to force minfi data into a MethyGenoSet object for use within the package methyAnalysis: Library(minfi) # mset is minfi object, e.g. used in dmpFinder code myexprs <- getM(mSet) mymeth <- getM ...
written 4.7 years ago by Lavinia Gordon480
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methyAnalysis - changes to GenoSet
... Dear Bioc users, I have just tried the example code supplied with the package methyAnalysis and am getting an error: > ################################################### > ### code chunk number 3: Slide-window smoothing of the DNA methylation data > ####################################### ...
genoset written 4.7 years ago by Lavinia Gordon480 • updated 4.7 years ago by Martin Morgan ♦♦ 20k
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Answer: A: Pre-processing and probe removal in lumi
... Hi Matt, Not sure about lumi, only use it for HM27 data (for which it is great), not sure how well it works with HM450. Take a look at the package minfi and also the annotation packages *450*, e.g. IlluminaHumanMethylation450k.db, Tim Triche Jr. has put some nice well-documented code in these vigne ...
written 4.8 years ago by Lavinia Gordon480
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Comment: C: VariantAnnotation - MatrixToSnpMatrix - only returns NAs
... Many thanks for this Valerie. I will look at genoTypeToSnpMatrix. With regards, 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 ww ...
written 4.8 years ago by Lavinia Gordon480
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Answer: A: VariantAnnotation - MatrixToSnpMatrix - only returns NAs
... Hi Valerie, Just one other thought, is it possible that MatrixToSnpMatrix() cannot work with unphased data? My VCF is unphased. If I change the file VariantAnnotation\extdata\chr22.vcf to unphased that gives all NA values. > vcf <- readVcf("chr22.vcf", "hg19") > calls <- geno(vcf)$GT ...
written 4.8 years ago by Lavinia Gordon480
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Comment: C: VariantAnnotation - MatrixToSnpMatrix - only returns NAs
... Hi Valerie, Thank you for your reply. I'll investigate the development branch option. I did see the warnings however I find it hard to believe that these should apply to every single entry in my VCF. With regards, Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformatics ...
written 4.8 years ago by Lavinia Gordon480
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VariantAnnotation - MatrixToSnpMatrix - only returns NAs
... Hi, I have just started working with VCF files and have discovered the VariantAnnotation package, many thanks for making these functions available. Following the code outlined in the reference manual for MatrixToSnpMatrix, my VCF returns only NA values: > head(geno(vcf)$GT) GHS008 GHS0 ...
written 4.8 years ago by Lavinia Gordon480
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geneplotter - buildChromLoc for arrays with no .db
... Hi Marc, No I haven't. Perfect, thanks for that, answers my question. I thought building a new db might be the way to go but wanted to check before getting started on it. Thanks a lot, Cheers, Lavinia. ------------------------------ Message: 9 Date: Fri, 07 Dec 2012 14:44:40 -0800 From: Marc Car ...
go geneplotter written 5.0 years ago by Lavinia Gordon480

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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