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Which input file is used for DGEList in EgdeR?
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biomaRt has encountered an unknown server error.
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[Bug] Segfault in edgeR::cpm
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8 months ago Jitendra ▴ 10
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PhD student
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10 months ago Nisha • 0
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create COMPOUND dataset (2 matrices) with rhdf5?
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Can the limma package be applied to Log2 RUV-normalized data?
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different number of DEG because of outliers
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limma: More differentially expressed genes when factor included in model than when used as blocking factor
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Confusion about LFC using contrasts weights in EdgeR
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Light difference when using coef vs omit a group when compare 3 groups.
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
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5 months ago kjngo ▴ 40
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7 months ago Federico ▴ 10
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Question about setting threshold using filtering by expression on genes in edgeR
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updated 9 months ago by 50k • written 7.9 years ago by • 0
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1,738 results • Page 2 of 35
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Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
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> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
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There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
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A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
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