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DGE
•
reset
0
votes
3
replies
300
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
9 weeks ago
ruba-mahmoud
• 0
1
vote
3
replies
378
views
Can CAMERA analyze just one particular pathway
pathway
ORA
limma
CAMERA
DGE
updated 3 months ago by
Gordon Smyth
48k • written 3 months ago by
manuelsokolov
• 0
0
votes
1
reply
288
views
How to do PFS after Voom + Limma DGE ?
RNASeqData
limma
voom
PFS
DGE
updated 5 months ago by
James W. MacDonald
64k • written 5 months ago by
manuelsokolov
• 0
0
votes
1
reply
548
views
DGE genes are not available in GSEA
dge
gsea
updated 11 months ago by
Guido Hooiveld
★ 3.8k • written 11 months ago by
Lawrence
• 0
5
votes
6
replies
1.3k
views
How to calculate dispersion DESeq2 - Step by Step
DGE
DESeq2
Differential
2.3 years ago • updated 2.2 years ago
Zeke Smith
▴ 10
1
vote
1
reply
615
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome
organoids
DGE
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
S
▴ 10
0
votes
1
reply
1.1k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 2.5 years ago by
Kevin Blighe
3.9k • written 2.5 years ago by
lkianmehr
• 0
1
vote
2
replies
727
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 3.4 years ago by
Gordon Smyth
48k • written 3.4 years ago by
June.
▴ 10
5
votes
10
replies
1.1k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2
DGE
contrast
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
llooll1
• 0
3
votes
8
replies
1.0k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 3.9 years ago by
James W. MacDonald
64k • written 3.9 years ago by
s.connell
• 0
0
votes
2
replies
727
views
Longitudinal Time-Course microarray experiment with two time points
edge
DGE
microarray
updated 4.0 years ago by
Gordon Smyth
48k • written 4.0 years ago by
joanasabinopinto
• 0
0
votes
5
replies
986
views
edgeR or DESeq2 between duplicated chromosomes in the same individual
deseq2
edgeR
normalization
DGE
updated 4.1 years ago by
Gordon Smyth
48k • written 4.1 years ago by
grant.dejong
• 0
0
votes
4
replies
2.3k
views
edgeR DGEList and design matrix
edger
DGE
updated 4.3 years ago by
Yunshun Chen
▴ 820 • written 4.3 years ago by
ctstackh
• 0
3
votes
7
replies
1.7k
views
How to determine the cause of no difference between treatments in rnaseq?
RNAseq
DGE
edger
updated 4.5 years ago by
Gordon Smyth
48k • written 4.5 years ago by
jdmontenegroc
• 0
0
votes
0
replies
793
views
quantifying piRNA and tRNA by Salmon
Salmon
DGE
5.0 years ago
lkianmehr
• 0
3
votes
4
replies
1.8k
views
DGE matrix annotation
DGE
DESeq2
AnnotationDbi
updated 5.2 years ago by
James W. MacDonald
64k • written 5.2 years ago by
maxininfa
• 0
0
votes
3
replies
1.5k
views
glmQLFTest, coef=2:4, decideTestDGE not working
edger
DGE
coef
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
rebeccajane93
• 0
4
votes
8
replies
1.6k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq
edger
DGE
no replicates
6.3 years ago
Stefany Solano
• 0
5
votes
4
replies
1.2k
views
Experiment design contrasts any time edgeR
DGE
rnaseq
RNA
edger
updated 6.5 years ago by
londonflavido
• 0 • written 6.5 years ago by
Pietro
▴ 40
12
votes
10
replies
6.0k
views
edgeR glmLRT with test="F"?
edger
dge
differential expression
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Ryan C. Thompson
7.8k
20 results • Page
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Replies
Comment: Problem loading HDF5Array in R 4.3.2
by
Mike Smith
★ 6.2k
Great, I'm glad it worked. It's frustrating that the binary doesn't work for you; that shouldn't happen! However I'm not sure how to go a…
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
No, I don't. Confirm that `geneList` has the expected format. What is the outcome of `geneList[1:5]`, `str(geneList)` and `class(geneList)…
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
Did you try it yourselves? But the answer is yes.
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
nromerov
• 0
Also do you know if the gaphical functions as dotplot, enrichmap and cnetplot works on this generic analysis? still sorry for bothering you
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
nromerov
• 0
Thank you very much for your help iu was really deseperate about this that i wasn't thinking too well yesterday im really gratefull with yo…
Votes
Comment: Problem loading HDF5Array in R 4.3.2
Answer: gseGO input list
Comment: Problem loading HDF5Array in R 4.3.2
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
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