User: Jenny Drnevich

gravatar for Jenny Drnevich
Jenny Drnevich1.9k
Reputation:
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Location:
United States
Last seen:
1 month, 1 week ago
Joined:
9 years, 8 months 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 • 251 results • page 1 of 26 • next >
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Comment: C: Problem with tximport(reader = read_tsv) and workaround
... Thanks - I'll try it out soon! ...
written 5 weeks ago by Jenny Drnevich1.9k
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Comment: C: EGSEA generateReport() error "no adj nodes"
... Hi Monther, I had updated all my packages in the last week or two, but I went ahead and updated again today but still had the same error with EGSEA 1.6.0. The new version hasn’t been pushed through yet, but I’ll check again tomorrow. Thanks for getting a workaround done so fast! It is weird that yo ...
written 6 weeks ago by Jenny Drnevich1.9k
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Comment: C: EGSEA generateReport() error "no adj nodes"
... Thanks! Please let me know when the bug is fixed. Jenny From: Monther Alhamdoosh [bioc] [mailto:noreply@bioconductor.org] Sent: Thursday, November 30, 2017 7:01 PM To: Zadeh, Jenny Drnevich <drnevich@illinois.edu> Subject: [bioc] A: EGSEA generateReport() error "no adj nodes" Activity on a ...
written 6 weeks ago by Jenny Drnevich1.9k
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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 7 weeks 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 7 weeks ago by Jenny Drnevich1.9k • updated 6 weeks 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 9 weeks 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 9 weeks ago by Jenny Drnevich1.9k • updated 9 weeks ago by James W. MacDonald45k
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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 9 weeks 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 9 weeks 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 9 weeks ago by Jenny Drnevich1.9k • updated 9 weeks ago by Gordon Smyth32k

Latest awards to Jenny Drnevich

Popular Question 10 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
Popular Question 22 months ago, created a question with more than 1,000 views. For biocLite() fails to update packages when main library not writable
Popular Question 22 months ago, created a question with more than 1,000 views. For biocLite() upgrade issue when same package in 2 libraries
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
Autobiographer 3.3 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.5 years ago, created 100 posts.

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