User: erin.gill81

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erin.gill8140
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40
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New User
Location:
Canada
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3 months ago
Joined:
5 years, 2 months ago
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e**********@gmail.com

Posts by erin.gill81

<prev • 17 results • page 1 of 2 • next >
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Comment: C: DESeq2: Paired multifactor test with batch effect - one or more variables in des
... Thank you so much for your quick answer! That makes perfect sense. ...
written 3 months ago by erin.gill8140
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DESeq2: Paired multifactor test with batch effect - one or more variables in design formula are linear combinations of others
... Hi, I'm analyzing an RNA-Seq data set and I would like to perform a paired multifactor test that incorporates batch effect. When I use the design formula ~ response + response:PID + response:timepoint then eliminate columns from the model matrix manually that contain only zeroes, DESeq2 will ...
deseq2 written 3 months ago by erin.gill8140 • updated 3 months ago by Michael Love26k
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Answer: A: DESeq2 Error in .Primitive("c")(<S4 object of class "GRangesList">
... Thank you for your response, Martin. I have also managed to fix the error by omitting parallel=TRUE from the last line of my code. Therefore, the issue may actually lie in the BiocParallel library. ...
written 2.7 years ago by erin.gill8140
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DESeq2 Error in .Primitive("c")(<S4 object of class "GRangesList">
... Hello, I am attempting to re-run a script to find differentially expressed genes using DESeq2 that ran correctly two days ago. Since then, I updated R from version 3.3.2 to version 3.3.3. When attempting to call the DESeq function today, I get the following error: Error in .Primitive("c")(<S4 ...
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Comment: C: DESeq2 Finding genotype effect to stimulation minus effect of not stimulating
... Thank you for your quick reply!   Erin ...
written 3.9 years ago by erin.gill8140
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DESeq2 Finding genotype effect to stimulation minus effect of not stimulating
... Hello, I'm attempting to compare RNA-Seq datasets where I have two different genotypes (WT and mutant) and two conditions (stimulated and unstimulated). I would like to determine which genes are only differentially expressed between the two genotypes upon stimulation, but are NOT differentially exp ...
deseq2 rna-seq written 3.9 years ago by erin.gill8140 • updated 3.9 years ago by Michael Love26k
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Answer: A: DESeq2 different results from similar datasets
... Thank you so much for your explanation. I really appreciate it. ...
written 4.0 years ago by erin.gill8140
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DESeq2 different results from similar datasets
... Hello, I'm analysing an RNA-Seq dataset where I have two cell lines (WT and mutant) and nine stimulation conditions. I want to find the condition effects for the mutant cell line (ie which genes are differentially expressed between the mutant and WT cells in each of the nine conditions). When I run ...
deseq2 differential gene expression rna-seq written 4.0 years ago by erin.gill8140
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DESeq2 Contrast and Design Matrix Question: 4 Experimental Factors
... Hello, I'm trying to analyse an RNA-Seq dataset using DESeq2 that has four experimental factors: disease, treatment, donor and sequencing run. This is my colData (C is control): treatment disease donor run R Disease ...
rnaseq deseq2 written 4.1 years ago by erin.gill8140 • updated 4.1 years ago by Michael Love26k
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Nested Comparison using DESeq2
... Hello,  I'm trying to analyse an RNA-seq dataset where I have three treatment levels, "early", "late", and "untreated". I would like to know how to do a nested comparison in DESeq2 such that I compare ((early Vs untreated) Vs (late Vs untreated)). I've pasted my code below: samples = read.csv("s ...
rnaseq deseq2 written 4.7 years ago by erin.gill8140 • updated 4.7 years ago by Ryan C. Thompson7.4k

Latest awards to erin.gill81

Great Question 2.6 years ago, created a question with more than 5,000 views. For 3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
Popular Question 2.6 years ago, created a question with more than 1,000 views. For DESeq2 different results from similar datasets
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Nested Comparison using DESeq2
Popular Question 4.0 years ago, created a question with more than 1,000 views. For 3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2

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