User: Jenny Drnevich

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Jenny Drnevich1.9k
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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 • 254 results • page 2 of 26 • next >
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Comment: C: GO-terms delivered by GOstats hyperGTest() do not exist in my universe
... I wouldn't necessarily want to remove all the parental terms because they could find higher level terms that have several different child terms. However, to reduce the redundancy in your testing, do  GSEAGOHyperGParams(conditional = TRUE) . This will test GO:0005747 first, and if it is significant t ...
written 3 months ago by Jenny Drnevich1.9k
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Answer: C: GO-terms delivered by GOstats hyperGTest() do not exist in my universe
... The reason you get GO terms in the output that did not seem to be in the input universe is because the input universe only contains specific annotated GO terms. The part of your code: goAllFrame <- GOAllFrame(goFrame) actually pulls in all parental terms of the specific annotated GO terms. Reme ...
written 3 months ago by Jenny Drnevich1.9k
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limma wsva() does not return what it says it will
... I've started to play around with limma's new wsva() function to generate surrogate variables. The help page says under Value: "Numeric matrix, same as design but with n.sv columns added containing the surrogate variables.". However, the actual value returned is just the surrogate variables, not the ...
limma written 3 months ago by Jenny Drnevich1.9k • updated 3 months ago by Gordon Smyth32k
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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 4 months 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$offset) as the lib.size in cpm() rather than lengthScaledTPM because my next question was going to be if prior.count = 3 was too large for lengthScaledTPM values, which sum to 1 million as opposed to normalize library sizes wh ...
written 4 months ago by Jenny Drnevich1.9k
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tximport recommendation for limma-trend downstream analysis?
... Hi there, I was looking through the vignette for tximport, and it has recommendations for how to import data for downstream analysis in edgeR, DESeq2 and limma-voom, but it does not mention the lesser-used limma-trend. The edgeR method stores the length corrections in y$offset, but the voom() funct ...
limma edger tximport limma-trend written 4 months ago by Jenny Drnevich1.9k • updated 4 months ago by Aaron Lun18k
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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 7 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 7 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 7 months ago by Jenny Drnevich1.9k • updated 7 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 9 months ago by Jenny Drnevich1.9k • updated 7 months ago by Gordon Smyth32k

Latest awards to Jenny Drnevich

Popular Question 11 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 23 months ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 23 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 2.6 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
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Centurion 3.6 years ago, created 100 posts.

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