User: gkuffel

gravatar for gkuffel
gkuffel10
Reputation:
10
Status:
New User
Location:
Loyola University
Last seen:
6 months ago
Joined:
1 year, 5 months ago
Email:
g******@luc.edu

I manage the Loyola Genomics Facility. A core that provides experimental design, library preparation, next generation sequencing, and bioinformatics to a broad user base.

Posts by gkuffel

<prev • 9 results • page 1 of 1 • next >
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Comment: C: DESeq2 Control for differences between patients
... Thank you for the response. So I do not see any differential expression when using design =~ condition and p-adj < 0.1. Is there anything else I can modify or try? Also, if I look at p values instead of p-adj then I see some differential expression (about 1000 genes). ...
written 6 months ago by gkuffel10
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DESeq2 Control for differences between patients
... Hi, I have a relatively simple RNA-Seq experiment. I have 10 samples in my control group and 10 samples in my treatment group. Each sample is from a different patient. How can I test for differences between control and treatment groups but control for the natural differences we might see between pa ...
deseq2 written 6 months ago by gkuffel10 • updated 6 months ago by swbarnes250
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Comment: C: DESeq2 Design Formula for Time Series Experiment
...   David, Thank you so much for your reply. I have a few more questions if you have time: 1. So with my current design (design =~ Timepoint + Patient) am I testing for differences between patients while controlling for variability caused by time? 2.  If I use the design: design = ~ Timepoint + Tr ...
written 11 months ago by gkuffel10
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DESeq2 Design Formula for Time Series Experiment
... Hi everyone, I have miRNA-Seq data for an experiment with the following parameters: SampleID     Treatment     Timepoint     Patient    P1_0                  TB                 0             1    P1_1                  TB                 1             1    P1_2                  TB               ...
deseq2 written 12 months ago by gkuffel10 • updated 12 months ago by David Requena20
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Comment: C: Sample not clustering as expected in DESeq2
... Thanks for your input Michael. ...
written 15 months ago by gkuffel10
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Answer: A: Sample not clustering as expected in DESeq2
... Thanks for your input Michael. ...
written 15 months ago by gkuffel10
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Sample not clustering as expected in DESeq2
... Hoping I can get some help. I have been using DESeq2 for several months now on several different projects (I manage a NGS core). For most of these projects, the samples do not cluster as I would expect. For example, not all of the treatments will cluster with the treament group and not all of the co ...
deseq2 euclidean sample distance written 15 months ago by gkuffel10
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Comment: A: Running DESeq2 inside local Galaxy instance
... Thanks, I was trying to get some input from the author of the tool, Michael Love and thought this forum would be the best place to reach him. ...
written 17 months ago by gkuffel10
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Running DESeq2 inside local Galaxy instance
... Hi everyone,   We have tried many times to install DESeq2 to our local instance of Galaxy. The install is successful but when we run the tool we get the following error:   Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in librar ...
deseq2 galaxy written 17 months ago by gkuffel10

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