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cpm
•
reset
2
votes
2
replies
326
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
10 weeks ago
sukeshinik5
▴ 20
5
votes
7
replies
1.6k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 18 months ago by
Gordon Smyth
52k • written 18 months ago by
mohammedtoufiq91
▴ 10
3
votes
9
replies
2.5k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
20 months ago
mohammedtoufiq91
▴ 10
5
votes
6
replies
2.4k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM
filterByExpr
edgeR
histogram
rowsums
2.0 years ago • updated 24 months ago
mohammedtoufiq91
▴ 10
2
votes
7
replies
1.9k
views
CPM after RUVseq
RUVSeq
CPM
Normalization
2.5 years ago
Jess
• 0
1
vote
1
reply
1.2k
views
Degust: what normalization method does it use
DEGUST
Normalization
CPM
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
Caroline
• 0
0
votes
2
replies
3.7k
views
CPM function in EDGER
edger
cpm
rnaseq
4.3 years ago
francesca3
• 0
0
votes
3
replies
914
views
Normalization of RNA seq data
RNA seq
cpm
updated 4.7 years ago by
Kevin Blighe
★ 4.0k • written 4.7 years ago by
isabel.pieterse
• 0
3
votes
2
replies
1.1k
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 4.7 years ago by
Rory Stark
★ 5.2k • written 4.7 years ago by
Guandong Shang
▴ 40
4
votes
5
replies
1.4k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2
vst
pca
cpm
4.8 years ago
svlachavas
▴ 840
1
vote
2
replies
1000
views
Should the rlog normalised gene expression counts be further normalised?
rlog
CPM
RKPM
updated 5.0 years ago by
Steve Lianoglou
★ 13k • written 5.0 years ago by
zhang.jianhai
▴ 10
5
votes
7
replies
3.0k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
5.5 years ago
altintas.ali
• 0
3
votes
2
replies
1.2k
views
How to calculate average log2 CPM with batch effect?
edger
limma
cpm
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
b.nota
▴ 370
2
votes
4
replies
1.6k
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger
cpm
non-specific filtering
rnaseq
updated 6.4 years ago by
Gordon Smyth
52k • written 6.4 years ago by
svlachavas
▴ 840
16
votes
6
replies
33k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 6.5 years ago by
ftroot1010
▴ 20 • written 6.7 years ago by
jxb.dev
▴ 40
6
votes
14
replies
3.4k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis
variancestabilizingtransformation
normalization
cpm
edger
updated 6.6 years ago by
Wolfgang Huber
★ 13k • written 6.6 years ago by
svlachavas
▴ 840
6
votes
2
replies
3.1k
views
edgeR cpm() function with and without log2
edger
cpm
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
b.nota
▴ 370
3
votes
8
replies
1.6k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT
CPM
lowcountgenes
deseq2
6.8 years ago
A
▴ 40
0
votes
3
replies
1.5k
views
edgeR:fitted and partial expression values
edgeR
cpm
edger
fitted model
explained variance
updated 6.9 years ago by
Gordon Smyth
52k • written 6.9 years ago by
alakatos
▴ 130
4
votes
11
replies
5.0k
views
edgeR cpm filter
edger
independent filtering
multiple factor design
cpm
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
teshome.dagnem
• 0
3
votes
9
replies
2.0k
views
edgeR long vectors support when normalizing abundance matrix
edger
cpm
7.2 years ago
jtremblay514
• 0
2
votes
7
replies
6.3k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
7.8 years ago
kkadzi25
• 0
1
vote
2
replies
2.2k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger
filtering
cpm
updated 8.3 years ago by
Gordon Smyth
52k • written 8.3 years ago by
lynski008
• 0
2
votes
7
replies
2.7k
views
About differentially expressed genes that found by edgeR
edgeR
DE analysis
fold change
cpm
updated 8.3 years ago by
Ryan C. Thompson
★ 7.9k • written 8.3 years ago by
Sara
▴ 20
1
vote
6
replies
1.9k
views
extracting cpm expression from limma fit
limma
cpm
updated 8.5 years ago by
José Luis Lavín
▴ 10 • written 8.8 years ago by
map2085
▴ 40
1
vote
3
replies
2.7k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2
rnaseq
rna-seq
normalization
cpm
updated 8.6 years ago by
Wolfgang Huber
★ 13k • written 8.6 years ago by
stwestreich
• 0
5
votes
4
replies
8.0k
views
edgeR cpm filter with >1 factor
edger
cpm
multiple factor design
independent filtering
8.9 years ago
dietahanson
▴ 30
13
votes
3
replies
3.8k
views
EdgeR cpm: factor of 2 when adjusting library size?
edger
cpm
9.0 years ago
mikaelhc
▴ 20
5
votes
3
replies
1.9k
views
Support for offsets in cpm and voom functions?
edgeR
cpm
voom
limma
9.2 years ago
Ryan C. Thompson
★ 7.9k
0
votes
3
replies
3.7k
views
CPM output from edgeR for a downstream application
CPM
edgeR
9.5 years ago
ycding
▴ 10
30 results • Page
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Comment: Can't post a question?
by
Aimee
• 0
I copied my text to a file in linux and ran: ```r grep --color='auto' -P -n "[^\x00-\x7F]" filename.txt ``` It highlighted everything that…
Answer: sva: get a sv for RIN scores
by
Gordon Smyth
52k
Surrogate variables are not constructed from known variates, so one doesn't get surrogate variables for RIN scores. I am guessing that the …
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
by
alexandra.casey
• 0
any update? It's still not working for me. I'm amazed it's taking this long to fix!
Comment: git push errors
by
Jiping Wang
▴ 90
I have bioconductor remote named "upstream". thanks for help!! I missed ":devel" after master. ``` (base) jon@Jipings-2021-macbook-pro Rib…
Answer: git push errors
by
James W. MacDonald
67k
This is a question for the bioc-devel listserv (bioc-devel@r-project.org) rather than the support site. However, it looks like you are s…
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Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
A: DESeq2 One-way ANOVA with 3 sample groups?
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