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filtering
•
reset
0
votes
2
replies
401
views
Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
3 months ago
gingergeiger22
• 0
0
votes
1
reply
668
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
updated 8 months ago by
Michael Love
43k • written 9 months ago by
smac_head
• 0
3
votes
11
replies
2.0k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 22 months ago by
Gordon Smyth
52k • written 22 months ago by
alexia.brunel
• 0
5
votes
7
replies
1.8k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 23 months ago by
Gordon Smyth
52k • written 23 months ago by
mohammedtoufiq91
▴ 10
5
votes
8
replies
2.6k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression
R
filtering
limma
2.6 years ago • updated 2.4 years ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
719
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
2.7 years ago
Fatemeh
• 0
3
votes
5
replies
2.7k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 5.1 years ago by
Michael Love
43k • written 5.1 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.4k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
5.3 years ago
jam526
• 0
2
votes
4
replies
2.6k
views
Filtering, minimum sample number, and condition in edgeR
edger
filtering
updated 6.4 years ago by
Ryan C. Thompson
★ 7.9k • written 6.4 years ago by
rproendo
▴ 30
0
votes
1
reply
1.2k
views
How to keep the genes whose counts are equal or greater than 10
deseq2
filtering
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 years ago by
n_h_78
• 0
1
vote
1
reply
1.1k
views
DeSeq2 independant filtering barely removes any genes
deseq2
differential gene expression
filtering
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
mnaymik
• 0
1
vote
2
replies
1.4k
views
Filtering Rna-seq counts
rna-seq
filtering
updated 6.9 years ago by
Gordon Smyth
52k • written 6.9 years ago by
Aurora
▴ 20
5
votes
12
replies
8.7k
views
Filtering step for differential analysis in edgeR
r
edger
differential gene expression
filtering
bioconductor
updated 7.0 years ago by
Gordon Smyth
52k • written 7.0 years ago by
Biologist
▴ 120
4
votes
8
replies
1.9k
views
edgeR error when trying to filter peaks with low read counts
edger
R
filtering
7.0 years ago
camerond
• 0
0
votes
2
replies
1.5k
views
Filtering genes with a minimum number of counts between samples
DESeq2
filtering
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
A
▴ 60
1
vote
1
reply
2.2k
views
Filtering a BED file according to genomic annotation
bed files
bedtools
filtering
chipseq
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
rbronste
▴ 60
0
votes
2
replies
2.0k
views
DiffBind remove low count intervals for differential analysis
diffbind
filtering
7.4 years ago
gasta88
• 0
0
votes
2
replies
1.3k
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind
dba.report
filtering
7.4 years ago
konstantopoulos
• 0
1
vote
3
replies
6.0k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2
filtering
outliers
count outliers
updated 7.7 years ago by
Wolfgang Huber
★ 13k • written 7.7 years ago by
heikki.sarin
▴ 10
1
vote
6
replies
2.3k
views
Nonspecific filtering of microarray data
microarray
affymetrix microarrays
pre-filtering
filtering
nonspecific filtering
updated 7.9 years ago by
Wolfgang Huber
★ 13k • written 7.9 years ago by
n.lu
• 0
2
votes
2
replies
1.3k
views
Limma filtering based on treatment group
limma
filtering
updated 7.9 years ago by
Steve Lianoglou
★ 13k • written 7.9 years ago by
jamie.gearing
▴ 60
3
votes
4
replies
1.6k
views
Any way to detach or simplify nested GRangesList ?
grangeslist
filtering
r
8.6 years ago
Jurat Shahidin
▴ 80
1
vote
2
replies
2.3k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger
filtering
cpm
updated 8.6 years ago by
Gordon Smyth
52k • written 8.6 years ago by
lynski008
• 0
6
votes
4
replies
2.1k
views
Filtering after a contrast
deseq2
r
filtering
bioconductor
updated 8.7 years ago by
Steve Lianoglou
★ 13k • written 8.7 years ago by
rattigak
• 0
0
votes
1
reply
1.3k
views
Does the normalization pipeline for scran include filtering out genes with low counts?
filtering
scran
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
amckenz
• 0
9
votes
11
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 8.8 years ago by
David ROUX
▴ 20 • written 8.9 years ago by
alireza_sharifian_10
▴ 20
5
votes
12
replies
2.5k
views
Filtering before the linear modelling and empirical bayes steps
DEG
Limma
Filtering
updated 9.1 years ago by
Ryan C. Thompson
★ 7.9k • written 9.1 years ago by
Shamim Sarhadi
▴ 20
2
votes
4
replies
2.5k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix
limma
filtering
updated 10.0 years ago by
James W. MacDonald
68k • written 10.0 years ago by
ablanchetcohen
• 0
2
votes
7
replies
3.1k
views
Different filters with edgeR
edger
filtering
10.1 years ago
cpcantalapiedra
• 0
3
votes
10
replies
2.9k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering
bioconductor
genesymbols
expressionset
10.1 years ago
svlachavas
▴ 840
30 results • Page
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Replies
Comment: RNA Seq using Lrt
by
Rob
• 0
So if I have understood what you have said : If i want to see if Day (time) has an effect / is being tested - then the reduced model should…
Comment: How to convert transcript counts to gene counts in R?
by
ben
• 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open!
by
Ali
• 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets
by
Gordon Smyth
52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install
by
Szabolcs
• 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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