User: rclaire

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rclaire0
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Posts by rclaire

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DESeq2 high variance in differential expression results
... Hello,  I have been using DESeq2 to analyze small RNA expression across several treatments. I am surprised to find in my results some sequences that have very high variance listed as significantly differentially expressed. I was under the impression that one of DESeq2's strengths is dealing with va ...
deseq2 differential gene expression lrt variance written 2.1 years ago by rclaire0 • updated 2.1 years ago by Ryan C. Thompson7.3k
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DESeq2 releveling not changing resultsNames options
... Hello, I have some questions about releveling to reset the factor level. I am running an experiment in DESeq2 with 4 stages that I want to compare to each other under one treatment. My goal is to change which factor is the reference for generating result outputs. I understand that the default is t ...
deseq2 multifactorial design relevel resultsnames written 3.2 years ago by rclaire0 • updated 3.2 years ago by Michael Love23k
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Answer: A: DESeq2 multifactor experiment design
... Hi Michael,  Thank you, that's been very helpful. I want to check on something about the filtering.  Since what I am doing is essentially pre-filtering, shouldn't I still keep the independentFiltering, instead of having it set to =FALSE in results? Or am I missing something? Here's how I've filte ...
written 3.3 years ago by rclaire0
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Answer: A: DESeq2 multifactor experiment design
... Hi Michael,  Thanks for the quick and helpful reply.  As for the comparisons within each stage I am interested in any differences across the treatments, not pairwise comparisons. I basically want to run an ANOVA for each stage, but having filtered and normalized the whole data set (all stages) tog ...
written 3.3 years ago by rclaire0
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DESeq2 multifactor experiment design
... Hello,   I am using DESeq2  on R (version 3.2.2) for analysis of small RNA expression data. I have some questions about how to set-up the experiment to answer the questions I am interested in.  I have a total of 80 samples. This consists of 4 different stages (ages) of fish embryo. At each stage, ...
deseq2 interactions contrast lrt multifactor written 3.3 years ago by rclaire0
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Answer: A: DESeq2 LRT output help
... Got it! Thanks, Michael. And sorry I didn't find it on my own first.  ...
written 4.0 years ago by rclaire0
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DESeq2 LRT output help
... Hello,  I am using DESeq2 to perform LRT analysis of a multi-treatment experiment, like an ANOVA. I have 5 different conditions, each with 4 replicates, and would like to generate a single p-value that indicates difference among the conditions, but not specific to any two conditions (as in a t-test ...
deseq2 anova lrt written 4.0 years ago by rclaire0
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R 3.2.0 problem with DESeq2 - Hmisc error
... Hi All, I was having compatibility issues with R and bioconductor, so I upgraded to the latest version of R (3.2.0) and am still having trouble. I am trying to install and use DESeq2. Please see the below output and errors. Any help would be greatly appreciated! Thanks, Claire   R version 3.2.0 ...
deseq2 software error R written 4.1 years ago by rclaire0 • updated 4.1 years ago by Steve Lianoglou12k

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For DESeq2 LRT output help
Popular Question 3.7 years ago, created a question with more than 1,000 views. For R 3.2.0 problem with DESeq2 - Hmisc error

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