User: Jenny Drnevich

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Jenny Drnevich1.9k
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9 years, 3 months ago
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d*******@illinois.edu

I work for the High Performance Biological Computing group (HPCBio) in the Carver Biotechnology Center at the University of Illinois, which is a core service center providing state-of-the-art infrastructure for genomic and proteomic research. My areas of expertise are statistical analyses of gene expression data from microarrays and RNA-Seq and post-analysis data mining. I also teach a a recurring workshop on how to analyze and data mine gene expression data.

Posts by Jenny Drnevich

<prev • 238 results • page 1 of 24 • next >
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Comment: C: prior.prob has opposite effects in goana and kegga?
... Thanks, Gordon! I've downloaded the new version and it's working as expected. Cheers, Jenny ...
written 5 weeks ago by Jenny Drnevich1.9k
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Answer: A: Plotting Gene Expression Data From Multiple Batches
... Use the removeBatchEffect() function to get data values suitable for visualization without the batch effects. Say you do your modeling like this where Data is an EList : fit <- lmFit(Data, design) To remove your batch effects, do: design2 <- model.matrix(~0+Class, data = phenot) no.batc ...
written 5 weeks ago by Jenny Drnevich1.9k
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bug in kegga() when using prior.prob?
... Hi all, I think there is a bug in the kegga() function when passing the prior.prob/trend argument. I came across this before when starting from the gometh() function with some methylation data and posted it to the support site here (https://support.bioconductor.org/p/96111/) but didn't get any answ ...
limma edger written 5 weeks ago by Jenny Drnevich1.9k • updated 5 weeks ago by Gordon Smyth31k
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prior.prob has opposite effects in goana and kegga?
... Hi all, I've come across some unexpected results when trying to go over-representation testing on array methylation data, which I've traced to the underlying goana() and kegga() functions from limma. Genes can have different numbers of CpGs, and so the gometh() function from missMethyl will by defa ...
limma goana kegga missmethyl gometh written 3 months ago by Jenny Drnevich1.9k • updated 5 weeks ago by Gordon Smyth31k
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Comment: C: raw probe set expression data and masking questions
... When you read in your cell files with read.celfiles(), did you set pkgname = to your new package name? Otherwise, it will pull in the regular package which could explain why you are still seeing them in the data. Jenny From: jacorvar [bioc] [mailto:noreply@bioconductor.org] Sent: Tuesday, March 28 ...
written 4 months ago by Jenny Drnevich1.9k
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Comment: C: goseq Error: could not find function "supportedOrganisms"
... install.packages() does not look in the Bioconductor repository by default. Use Bioconductor's install function and capitalize the package name properly: source("https://bioconductor.org/biocLite.R") biocLite("goseq") ...
written 4 months ago by Jenny Drnevich1.9k
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Comment: C: raw probe set expression data and masking questions
... I'm not sure, as I haven't worked with Affy data in a very long time. Looking at the oligo package, if there was just a single set of probes you know you wanted to remove, you could potentially build your own platform design information package with pdInfoBuilder http://bioconductor.org/packages/rel ...
written 4 months ago by Jenny Drnevich1.9k
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read.metharray() not recognizing some of my EPIC arrays; force = TRUE not working either
... Hi, I'm trying to use minfi's read.metharray.exp() / read.metharray() to read in 48 samples from 6 Illumina EPIC arrays. The arrays were all ordered at the same time from Illumina, but appear to come from two different main batches: two arrays have Sentrix_IDs 20111453005X and the other four arrays ...
minfi written 4 months ago by Jenny Drnevich1.9k
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bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
... Hi all, I've been following the F1000 tutorial on analyzing methylation array data (thanks to all involved in the paper and the packages - it's an amazing resource as I start my foray into methylation arrays!!) and their code now produces an error when running cpg.annotate(). I was able to track it ...
minfi dmrcate written 4 months ago by Jenny Drnevich1.9k • updated 4 months ago by Tim Peters60
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Comment: C: Easy way to turn OrgDb object from AnnotationHub into package?
... Hi Valarie, Setting PkgTemplate = "NCBIORG.DB" led to the following error: > seed <- new("AnnDbPkgSeed", Package = "org.Ng.eg.db", + Version = "0.0.1", Author = "Jenny Drnevich", + Maintainer = "Jenny Drnevich <drnevich@illinois.edu>", + PkgTempl ...
written 6 months ago by Jenny Drnevich1.9k

Latest awards to Jenny Drnevich

Popular Question 5 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 17 months ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 17 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 2.1 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Autobiographer 2.9 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.1 years ago, created 100 posts.

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