User: Jenny Drnevich

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Jenny Drnevich1.9k
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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 • 268 results • page 1 of 27 • next >
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cqn vignette error
... I recently started using the cqn package and have found a small error in the [vignette][1]. In code chunk 17, the glm.offset is put into the `d.mont `object and then `estimateGLMCommonDisp` is run to create a new object `d.mont.cqn`: ``` ################################################### ### code ...
normalization edger cqn written 6 hours ago by Jenny Drnevich1.9k
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Comment: C: BioC2018 Workshop book not linked from Bioconductor.org?
... Thanks! I do want to point out a possible issue I see arising after a new book is made for BioC 2019 - this git link isn't versioned, but presumably we'd want to keep the 2018 version somewhere even though the main https://bioconductor.github.io/BiocWorkshops/ will always point to the most recent ve ...
written 8 months ago by Jenny Drnevich1.9k
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BioC2018 Workshop book not linked from Bioconductor.org?
... Hi all, I really liked how the BioC2018 workshop materials were organized into a bookdown [book on GitHub](https://bioconductor.github.io/BiocWorkshops/). However, I don't see any links to this resource from the main [Bioconductor.org website](https://bioconductor.org/) in the Learn box, or the [He ...
conference website book written 8 months ago by Jenny Drnevich1.9k • updated 8 months ago by kayla.interdonato40
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Comment: C: Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
... HI Gordon, Thanks for the informative description - it makes better sense now. I do actually prefer the limma-trend pipeline, particularly for experiments with several contrasts due to it's ease of use.  But occasionally I get a simple 2-group experiment and then I use glmQLFit(). I do like to incr ...
written 12 months ago by Jenny Drnevich1.9k
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Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
... Hello! I noticed in edgeR's NEWS that for the just-released edgeR 3.24.0:  The default value for prior.count increased from 0.25 to 2 in cpm() and rpkm(). The new value is more generally useful and agrees with the default values in aveLogCPM() and with the DGEList method for plotMDS() I agr ...
edger prior.count written 13 months ago by Jenny Drnevich1.9k • updated 12 months ago by Gordon Smyth39k
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Comment: C: Bioconductor 3.8 is released
... Ah – now I see the message! You have to explicitly load the BiocManager package. The main install page and all the package landing pages call the install via BiocManager::install(), which as you said is silent. Probably would be good to add the warning to this as well when you get the chance. As al ...
written 13 months ago by Jenny Drnevich1.9k • updated 13 months ago by Martin Morgan ♦♦ 24k
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Comment: C: Bioconductor 3.8 is released
... Yes - I happen to be teaching a workshop tomorrow on Bioconductor, and the new way to upgrade to BioC took me a while to find. Previously, biocLite() would check and give a message that a newer version of Bioconductor was available for your version of R, but it doesn't like BiocManager::install() ha ...
written 13 months ago by Jenny Drnevich1.9k
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Comment: C: Easy way to turn OrgDb object from AnnotationHub into package?
... There are different levels of annotation... NCBI does have a genome for Plasmopara halstedii and it has 15,469 predicted proteins (https://www.ncbi.nlm.nih.gov/genome/?term=Plasmopara+halstedii). So there should be the locations for the exons making up these proteins in the .gff file, which is one l ...
written 15 months ago by Jenny Drnevich1.9k
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Comment: C: csaw: how to hack filtering windows by negative input controls?
... Hi Aaron, Thanks for your reply. I may try to run through your simulations to see if our dispersions get inflated, but I don’t have a ton of time before the BioC conference next week (and I have to write up my poster on a different experiment!). Maybe we can chat briefly about it in Toronto, if you ...
written 16 months ago by Jenny Drnevich1.9k
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csaw: how to hack filtering windows by negative input controls?
... Hi all, Aaron - thank you for the excellent csaw package and extensive users guide! I am analyzing a ChIPSeq experiment that has 60 IP samples + 60 inputs. There are 3 treatments X 4 brain regions = 12 groups X 5 reps each. It seems a shame not to use the input samples and I was following section 3 ...
csaw written 16 months ago by Jenny Drnevich1.9k • updated 16 months ago by Aaron Lun25k

Latest awards to Jenny Drnevich

Popular Question 12 months ago, created a question with more than 1,000 views. For goseq KEGG testing?
Popular Question 12 months ago, created a question with more than 1,000 views. For Problem with tximport(reader = read_tsv) and workaround
Popular Question 12 months ago, created a question with more than 1,000 views. For Problem using biocLite() to update packages
Popular Question 12 months ago, created a question with more than 1,000 views. For Limma, model with several factors
Popular Question 13 months ago, created a question with more than 1,000 views. For goseq KEGG testing?
Popular Question 13 months ago, created a question with more than 1,000 views. For Problem with tximport(reader = read_tsv) and workaround
Popular Question 19 months ago, created a question with more than 1,000 views. For trouble using select() to get all GO terms when have duplicate query IDs
Great Question 2.5 years ago, created a question with more than 5,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 2.5 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 2.8 years ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 3.7 years ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 3.7 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 4.4 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 5.4 years ago, created 100 posts.

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