User: Jenny Drnevich

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Jenny Drnevich1.9k
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9 years, 5 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 • 241 results • page 1 of 25 • next >
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Comment: C: tximport recommendation for limma-trend downstream analysis?
... Good to know! I probably would have figured that out once I had data in hand. I’ve got 4-6 transcriptome assemblies + Salmon counts coming in soon, so I’ll get lots of practice with tximport. Thanks for a great package!! Jenny From: Michael Love [bioc] [mailto:noreply@bioconductor.org] Sent: Friday ...
written 24 days ago by Jenny Drnevich1.9k
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Comment: C: tximport recommendation for limma-trend downstream analysis?
... Thanks, everyone! I like the idea of directly giving the counts and exp(y$offset) as the lib.size in cpm() rather than lengthScaledTPM because my next question was going to be if prior.count = 3 was too large for lengthScaledTPM values, which sum to 1 million as opposed to normalize library sizes wh ...
written 24 days ago by Jenny Drnevich1.9k
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tximport recommendation for limma-trend downstream analysis?
... Hi there, I was looking through the vignette for tximport, and it has recommendations for how to import data for downstream analysis in edgeR, DESeq2 and limma-voom, but it does not mention the lesser-used limma-trend. The edgeR method stores the length corrections in y$offset, but the voom() funct ...
limma edger tximport limma-trend written 24 days ago by Jenny Drnevich1.9k • updated 24 days ago by Aaron Lun16k
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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 3 months 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 3 months 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 3 months ago by Jenny Drnevich1.9k • updated 3 months ago by Gordon Smyth32k
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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 5 months ago by Jenny Drnevich1.9k • updated 3 months ago by Gordon Smyth32k
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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 6 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 6 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 6 months ago by Jenny Drnevich1.9k

Latest awards to Jenny Drnevich

Popular Question 7 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 19 months ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 19 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 2.3 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Autobiographer 3.1 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.3 years ago, created 100 posts.

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