User: j.viana

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j.viana0
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Posts by j.viana

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Comment: A: DESeq2: Outliers, covariates and number of replicates
... I got around it by running the model without covariates, extract the replaces counts and re-run the model with the covariates. Since in my model with RUV estimates there will be absolutely no replacement of outliers of exclusion of genes I feel this is ok. But I think something should be added to t ...
written 2.8 years ago by j.viana0
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Comment: A: DESeq2: Outliers, covariates and number of replicates
... I don't want to go on a tangent here, but I did use the quasi likelihood framework from edgeR, which did not solve the problem. My guess is that these genes do not have outlying dispersions.  ...
written 2.8 years ago by j.viana0
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DESeq2: Outliers, covariates and number of replicates
... Hi, I'm analysing RNA-seq data and I switched from edgeR to DESeq2 because most of my differentially expressed genes had an outlier sample, which was not an outlier in the entire dataset (judged by PCA and overall Cook's distance). My question is related to the criteria used by DESeq2 to count the ...
deseq2 ruvseq covariates batch cookscutoff written 2.8 years ago by j.viana0

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