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Experiment design contrasts any time edgeR
DGE
rnaseq
RNA
edger
updated 7.0 years ago by
londonflavido
• 0 • written 7.0 years ago by
Pietro
▴ 40
5
votes
6
replies
1.6k
views
How to calculate dispersion DESeq2 - Step by Step
DGE
DESeq2
Differential
2.7 years ago
Zeke Smith
▴ 10
3
votes
7
replies
2.3k
views
How to determine the cause of no difference between treatments in rnaseq?
RNAseq
DGE
edger
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
jdmontenegroc
• 0
0
votes
4
replies
2.7k
views
edgeR DGEList and design matrix
edger
DGE
updated 4.7 years ago by
Yunshun Chen
▴ 840 • written 4.7 years ago by
ctstackh
• 0
4
votes
8
replies
1.8k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq
edger
DGE
no replicates
6.7 years ago
Stefany Solano
• 0
3
votes
8
replies
1.2k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
s.connell
• 0
5
votes
10
replies
1.3k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2
DGE
contrast
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
llooll1
• 0
1
vote
2
replies
876
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
June.
▴ 10
7
votes
6
replies
453
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
0
votes
1
reply
456
views
How to do PFS after Voom + Limma DGE ?
RNASeqData
limma
voom
PFS
DGE
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
manuelsokolov
• 0
12
votes
10
replies
6.5k
views
edgeR glmLRT with test="F"?
edger
dge
differential expression
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
3
replies
1.7k
views
glmQLFTest, coef=2:4, decideTestDGE not working
edger
DGE
coef
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
rebeccajane93
• 0
1
vote
5
replies
1.2k
views
edgeR or DESeq2 between duplicated chromosomes in the same individual
deseq2
edgeR
normalization
DGE
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
grant.dejong
▴ 10
0
votes
2
replies
864
views
Longitudinal Time-Course microarray experiment with two time points
edge
DGE
microarray
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
joanasabinopinto
• 0
0
votes
1
reply
1.6k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 2.9 years ago by
Kevin Blighe
★ 3.9k • written 2.9 years ago by
lkianmehr
• 0
3
votes
4
replies
1.9k
views
DGE matrix annotation
DGE
DESeq2
AnnotationDbi
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
maxininfa
• 0
1
vote
3
replies
641
views
Can CAMERA analyze just one particular pathway
pathway
ORA
limma
CAMERA
DGE
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
manuelsokolov
• 0
0
votes
3
replies
493
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE
DESeq2
7 months ago
ruba-mahmoud
• 0
1
vote
1
reply
713
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome
organoids
DGE
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
S
▴ 10
0
votes
1
reply
812
views
DGE genes are not available in GSEA
dge
gsea
updated 16 months ago by
Guido Hooiveld
★ 3.9k • written 17 months ago by
Lawrence
• 0
0
votes
0
replies
902
views
quantifying piRNA and tRNA by Salmon
Salmon
DGE
5.5 years ago
lkianmehr
• 0
21 results • Page
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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