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cpm
•
reset
2
votes
2
replies
533
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
7 months ago
sukeshinik5
▴ 20
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
3
votes
9
replies
2.9k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
2.1 years ago
mohammedtoufiq91
▴ 10
5
votes
6
replies
2.9k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM
filterByExpr
edgeR
histogram
rowsums
2.4 years ago
mohammedtoufiq91
▴ 10
2
votes
7
replies
2.1k
views
CPM after RUVseq
RUVSeq
CPM
Normalization
2.9 years ago
Jess
• 0
1
vote
1
reply
1.3k
views
Degust: what normalization method does it use
DEGUST
Normalization
CPM
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
Caroline
• 0
0
votes
2
replies
3.9k
views
CPM function in EDGER
edger
cpm
rnaseq
4.7 years ago
francesca3
• 0
0
votes
3
replies
1.2k
views
Normalization of RNA seq data
RNA seq
cpm
updated 5.0 years ago by
Kevin Blighe
★ 4.0k • written 5.0 years ago by
isabel.pieterse
• 0
3
votes
2
replies
1.2k
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind
CPM
TMM
updated 5.1 years ago by
Rory Stark
★ 5.2k • written 5.1 years ago by
Guandong Shang
▴ 40
4
votes
5
replies
1.5k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2
vst
pca
cpm
5.2 years ago
svlachavas
▴ 840
1
vote
2
replies
1.1k
views
Should the rlog normalised gene expression counts be further normalised?
rlog
CPM
RKPM
updated 5.4 years ago by
Steve Lianoglou
★ 13k • written 5.4 years ago by
zhang.jianhai
▴ 10
5
votes
7
replies
3.3k
views
logCPM to CPM conversion after removeBatchEffect()
edger
removeBatchEffect
cpm
logCPM
limma
5.9 years ago
altintas.ali
• 0
3
votes
2
replies
1.4k
views
How to calculate average log2 CPM with batch effect?
edger
limma
cpm
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
b.nota
▴ 370
2
votes
4
replies
1.8k
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger
cpm
non-specific filtering
rnaseq
updated 6.8 years ago by
Gordon Smyth
52k • written 6.8 years ago by
svlachavas
▴ 840
19
votes
6
replies
35k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 6.9 years ago by
ftroot1010
▴ 20 • written 7.1 years ago by
jxb.dev
▴ 40
6
votes
14
replies
3.7k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis
variancestabilizingtransformation
normalization
cpm
edger
updated 7.0 years ago by
Wolfgang Huber
★ 13k • written 7.0 years ago by
svlachavas
▴ 840
6
votes
2
replies
3.3k
views
edgeR cpm() function with and without log2
edger
cpm
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
b.nota
▴ 370
3
votes
8
replies
1.8k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT
CPM
lowcountgenes
deseq2
7.2 years ago
A
▴ 60
0
votes
3
replies
1.6k
views
edgeR:fitted and partial expression values
edgeR
cpm
edger
fitted model
explained variance
updated 7.3 years ago by
Gordon Smyth
52k • written 7.3 years ago by
alakatos
▴ 130
4
votes
11
replies
5.3k
views
edgeR cpm filter
edger
independent filtering
multiple factor design
cpm
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
teshome.dagnem
• 0
3
votes
9
replies
2.2k
views
edgeR long vectors support when normalizing abundance matrix
edger
cpm
7.5 years ago
jtremblay514
• 0
2
votes
7
replies
7.4k
views
Gene Expression Matrix (CPM)
cpm
gene expression matrix
tmm
normailzation
8.2 years ago
kkadzi25
• 0
1
vote
2
replies
2.4k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger
filtering
cpm
updated 8.7 years ago by
Gordon Smyth
52k • written 8.7 years ago by
lynski008
• 0
2
votes
7
replies
2.9k
views
About differentially expressed genes that found by edgeR
edgeR
DE analysis
fold change
cpm
updated 8.7 years ago by
Ryan C. Thompson
★ 7.9k • written 8.7 years ago by
Sara
▴ 20
1
vote
6
replies
2.1k
views
extracting cpm expression from limma fit
limma
cpm
updated 8.9 years ago by
José Luis Lavín
▴ 10 • written 9.1 years ago by
map2085
▴ 40
1
vote
3
replies
3.0k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2
rnaseq
rna-seq
normalization
cpm
updated 9.0 years ago by
Wolfgang Huber
★ 13k • written 9.0 years ago by
stwestreich
• 0
5
votes
4
replies
8.4k
views
edgeR cpm filter with >1 factor
edger
cpm
multiple factor design
independent filtering
9.3 years ago
dietahanson
▴ 30
13
votes
3
replies
4.1k
views
EdgeR cpm: factor of 2 when adjusting library size?
edger
cpm
9.3 years ago
mikaelhc
▴ 20
5
votes
3
replies
2.0k
views
Support for offsets in cpm and voom functions?
edgeR
cpm
voom
limma
9.6 years ago
Ryan C. Thompson
★ 7.9k
0
votes
3
replies
3.8k
views
CPM output from edgeR for a downstream application
CPM
edgeR
9.9 years ago
ycding
▴ 10
30 results • Page
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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