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

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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 4 weeks 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 5 weeks ago by Jenny Drnevich1.9k • updated 5 weeks ago by Gordon Smyth35k
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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 6 weeks ago by Jenny Drnevich1.9k • updated 6 weeks ago by Martin Morgan ♦♦ 22k
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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 6 weeks 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 3 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 5 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 5 months ago by Jenny Drnevich1.9k • updated 5 months ago by Aaron Lun21k
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Comment: C: Hotels for BioC 2018?
... Thank you! My trip is book. See you this summer… From: Martin Morgan [bioc] <noreply@bioconductor.org> Sent: Wednesday, April 18, 2018 10:27 AM To: Zadeh, Jenny Drnevich <drnevich@illinois.edu> Subject: [bioc] C: Hotels for BioC 2018? Activity on a post you are following on support.bio ...
written 8 months ago by Jenny Drnevich1.9k
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Comment: C: Hotels for BioC 2018?
... Hi Martin, That’s fine, although it could be more explicitly stated on the registration page. Additionally, there is no other location information other than the University of Toronto, which has 3 different campuses. Is this at the downtown St. George Campus? Do you know the building name/side of c ...
written 8 months ago by Jenny Drnevich1.9k • updated 8 months ago by Martin Morgan ♦♦ 22k
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Hotels for BioC 2018?
... Hello, Is there going to be any hotel/accommodation information for BioC2018? I need to let my department know about estimated costs to get approval to attend. I'd like to start planning my trip soon! Thanks, Jenny ...
conference bioc2018 written 8 months ago by Jenny Drnevich1.9k • updated 8 months ago by Martin Morgan ♦♦ 22k

Latest awards to Jenny Drnevich

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Problem with tximport(reader = read_tsv) and workaround
Popular Question 6 weeks ago, created a question with more than 1,000 views. For goseq KEGG testing?
Popular Question 7 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
Popular Question 18 months ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Great Question 18 months ago, created a question with more than 5,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 21 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
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 2.8 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 3.4 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Autobiographer 4.2 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.4 years ago, created 100 posts.

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