Bioconductor ERCC

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1.1k

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ImpulseDE2 ImpulseDE ERCC RUVSeq

3.6 years ago • updated 3.5 years ago Mallory ▴ 10

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3.8k

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ERCC rna-seq edgeR tmm normalised values

updated 8.2 years ago by Aaron Lun ★ 28k • written 8.2 years ago by what_theheck24 • 0

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16k

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RNAseq deseq2 ercc

updated 8.6 years ago by Simon Anders ★ 3.8k • written 8.6 years ago by mbeckste ▴ 30

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8.3k

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limma voom deseq normalization ercc

updated 9.5 years ago by Gordon Smyth 52k • written 9.5 years ago by komal.rathi ▴ 120

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5.9k

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edger ercc

10.5 years ago John ▴ 10

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3.3k

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seqc rsubread featurecounts subjunc ercc News

10.5 years ago Wei Shi ★ 3.6k

6 results • Page 1 of 1

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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k

Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…

Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0

Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…

Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0

The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …

Comment: parameters of filterByExpr by Paul Harrison ▴ 110

It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k

voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…

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Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

GAlignments Cigar to GRanges

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