User: Jenny Drnevich

gravatar for Jenny Drnevich
Jenny Drnevich1.9k
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United States
Last seen:
4 days, 4 hours ago
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10 years, 1 month ago
Email:
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 • 258 results • page 2 of 26 • next >
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Comment: C: EGSEA generateReport() error "no adj nodes"
... Update: I tried running the example mouse data in the EGSEA123 workflow and had the same error right at the Build GO DAG topology step: > generateReport(gsa, number = 20, report.dir="./") EGSEA HTML report is being generated ... ##------ Thu Nov 30 16:29:59 2017 ------## Number of used cores ...
written 6 months ago by Jenny Drnevich1.9k
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EGSEA generateReport() error "no adj nodes"
... Hello, I am running through the EGSEA123 workflow, except I am using my own human data, consisting of 14K Entrez IDs, all of which are in org.Hs.eg.db. Everything goes fine until I try to generate the report when I get an error during the Build GO DAG topology and some additional warnings: librar ...
egsea egsea123 written 6 months ago by Jenny Drnevich1.9k • updated 6 months ago by Monther Alhamdoosh40
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Comment: C: Problem using biocLite() to update packages
... Yep, stupid Windows! That must be the cause of the random packages not being able to update. I’ll try to remember to shut down my CrashPlan before updating in the future. Cheers, From: James W. MacDonald [bioc] [mailto:noreply@bioconductor.org] Sent: Friday, November 10, 2017 4:20 PM To: Zadeh, Je ...
written 7 months ago by Jenny Drnevich1.9k
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Problem using biocLite() to update packages
... Hi all, I've had a weird thing happen occasionally in the past when using biocLite() to update packages and it just happened again and I finally had time to ask about it. I had upgraded everything to BioC 3.6 last week with no trouble. I just noticed today that the orgDB packages didn't get updated ...
variantannotation biocinstaller bioclite written 7 months ago by Jenny Drnevich1.9k • updated 7 months ago by James W. MacDonald46k
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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 7 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 7 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 7 months ago by Jenny Drnevich1.9k • updated 7 months ago by Gordon Smyth33k
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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 8 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$offset) as the lib.size in cpm() rather than lengthScaledTPM because my next question was going to be if prior.count = 3 was too large for lengthScaledTPM values, which sum to 1 million as opposed to normalize library sizes wh ...
written 8 months ago by Jenny Drnevich1.9k
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tximport recommendation for limma-trend downstream analysis?
... Hi there, I was looking through the vignette for tximport, and it has recommendations for how to import data for downstream analysis in edgeR, DESeq2 and limma-voom, but it does not mention the lesser-used limma-trend. The edgeR method stores the length corrections in y$offset, but the voom() funct ...
limma edger tximport limma-trend written 8 months ago by Jenny Drnevich1.9k • updated 8 months ago by Aaron Lun19k

Latest awards to Jenny Drnevich

Popular Question 6 weeks 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 12 months ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Great Question 12 months ago, created a question with more than 5,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 15 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() 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
Popular Question 3.0 years ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.9 years ago, created 100 posts.

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