User: gkuffel

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gkuffel10
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New User
Location:
Loyola University
Last seen:
3 months, 2 weeks ago
Joined:
2 years 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 • 12 results • page 1 of 2 • next >
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Comment: C: DESeq2 Design Formula
... Original post: https://support.bioconductor.org/p/100729/ ...
written 3 months ago by gkuffel10
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Comment: C: DESeq2 Design Formula
... Thanks Michael. I will add the link. Also I actually have 36 patients that received the treatments and two healthy controls per patient, I was just trying to show a simplified version. So your advice is to use Limma instead of DESeq2? ...
written 3 months ago by gkuffel10
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DESeq2 Design Formula
... Hello community, I have posted this question before but wanted to see if I can gain additional clarity. I have an miRNA experiment with the following parameters: SampleID     Treatment     Timepoint     Patient    P1_0                  TB                 0             1    P1_1                   ...
deseq2 michael love written 3 months ago by gkuffel10 • updated 3 months ago by Michael Love22k
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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 13 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 13 months ago by gkuffel10 • updated 13 months ago by swbarnes2150
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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 19 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 19 months ago by gkuffel10 • updated 19 months ago by David Requena20
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Comment: C: Sample not clustering as expected in DESeq2
... Thanks for your input Michael. ...
written 22 months ago by gkuffel10
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Answer: A: Sample not clustering as expected in DESeq2
... Thanks for your input Michael. ...
written 22 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 22 months ago by gkuffel10

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