Showing : expression • reset
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Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
2.7 years ago • updated 2.5 years ago mohammedtoufiq91 ▴ 10
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
2.8 years ago Jonathan • 0
0
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1
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1.5k
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Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 3.8 years ago by ▴ 80 • written 3.9 years ago by ▴ 10
1
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1
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1.6k
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Table expression data from GEO file
GEO expression GEOquery
updated 5.1 years ago by ★ 3.4k • written 5.1 years ago by • 0
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9
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2.7k
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Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs RNA-Seq Isoforms DTU expression
updated 5.9 years ago by ▴ 20 • written 5.9 years ago by • 0
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2
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977
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Two factors design with DESEq2
deseq2 genes expression
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
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3
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Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 10
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6
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1.8k
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variancePartition - testing for individuals
variance formula expression
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 30
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1.8k
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Job: Research Associate, Cambridge, UK - Oesophageal Cancer ICGC project
job sequencing methylation expression Job
10.3 years ago Andy Lynch ▴ 120
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Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes expression affymetrix pd.hugene.2.0.st limma
updated 10.3 years ago by 52k • written 10.3 years ago by ▴ 200
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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…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Votes
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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