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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 4.8 years ago by
Yunshun Chen
▴ 840 • written 4.8 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
6.8 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
42k • written 3.9 years ago by
llooll1
• 0
1
vote
2
replies
891
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
471
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Amit
• 0
0
votes
1
reply
470
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 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 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 4.6 years ago by
grant.dejong
▴ 10
0
votes
2
replies
872
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 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 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
661
views
Can CAMERA analyze just one particular pathway
pathway
ORA
limma
CAMERA
DGE
updated 8 months ago by
Gordon Smyth
50k • written 9 months ago by
manuelsokolov
• 0
0
votes
3
replies
504
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
723
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome
organoids
DGE
DESeq2
updated 2.9 years ago by
Michael Love
42k • written 2.9 years ago by
S
▴ 10
0
votes
1
reply
832
views
DGE genes are not available in GSEA
dge
gsea
updated 17 months ago by
Guido Hooiveld
★ 4.0k • written 17 months ago by
Lawrence
• 0
0
votes
0
replies
905
views
quantifying piRNA and tRNA by Salmon
Salmon
DGE
5.5 years ago
lkianmehr
• 0
21 results • Page
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Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Guido Hooiveld
★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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