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Showing :
expression
•
reset
5
votes
8
replies
2.7k
views
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
0
votes
0
replies
710
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
2.8 years ago
Jonathan
• 0
0
votes
1
reply
1.5k
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 3.8 years ago by
Konstantinos Yeles
▴ 80 • written 3.9 years ago by
mohammedtoufiq91
▴ 10
1
vote
1
reply
1.6k
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 5.1 years ago by
Robert Castelo
★ 3.4k • written 5.1 years ago by
lsbew
• 0
1
vote
9
replies
2.7k
views
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
fruce_ki
▴ 20 • written 5.9 years ago by
UserAnonyme
• 0
1
vote
2
replies
977
views
Two factors design with DESEq2
deseq2
genes
expression
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
UserAnonyme
• 0
7
votes
3
replies
4.3k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
kushshah
▴ 10
0
votes
6
replies
1.8k
views
variancePartition - testing for individuals
variance
formula
expression
updated 6.3 years ago by
mikhael.manurung
▴ 280 • written 6.3 years ago by
rina
▴ 30
0
votes
0
replies
1.8k
views
Job:
Research Associate, Cambridge, UK - Oesophageal Cancer ICGC project
job
sequencing
methylation
expression
Job
10.3 years ago
Andy Lynch
▴ 120
6
votes
5
replies
2.2k
views
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
Gordon Smyth
52k • written 10.3 years ago by
Paulo Nuin
▴ 200
10 results • Page
1 of 1
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Replies
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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