User: erin.gill81

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erin.gill8130
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Canada
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7 months ago
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3 years, 1 month ago
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e**********@gmail.com

Posts by erin.gill81

<prev • 15 results • page 1 of 2 • next >
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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 8 months ago by erin.gill8130
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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 22 months ago by erin.gill8130
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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 22 months ago by erin.gill8130 • updated 22 months ago by Michael Love15k
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Answer: A: DESeq2 different results from similar datasets
... Thank you so much for your explanation. I really appreciate it. ...
written 24 months ago by erin.gill8130
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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 24 months ago by erin.gill8130
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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 2.1 years ago by erin.gill8130 • updated 2.1 years ago by Michael Love15k
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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 2.6 years ago by erin.gill8130 • updated 2.6 years ago by Ryan C. Thompson6.1k
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Comment: C: 3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
... Thanks! I had confused two plotPCA functions that were part of different software packages. I've successfully used the code you provided with FactoMineR to generate the additional principal components I was looking for. Erin ...
written 2.6 years ago by erin.gill8130
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3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
... Hello,  I'm analysing an RNA-seq dataset using DESeq2, and would like to inspect the top three principal components on a 3D PCA plot. I know that the plot PCA function has been implemented in DESeq 2, but I've been unable to get the 3rd principal component to plot, print to screen or file. I've pas ...
rnaseq deseq2 pca written 2.6 years ago by erin.gill8130 • updated 2.6 years ago by Michael Love15k

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