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5
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6
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466
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How to calculate dispersion DESeq2 - Step by Step
DGE
DESeq2
Differential
8 months ago
Zeke Smith
▴ 10
1
vote
1
reply
305
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome
organoids
DGE
DESeq2
updated 11 months ago by
Michael Love
36k • written 11 months ago by
S
▴ 10
0
votes
1
reply
333
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 11 months ago by
Kevin Blighe
3.5k • written 11 months ago by
lkianmehr
• 0
1
vote
2
replies
322
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 22 months ago by
Gordon Smyth
45k • written 22 months ago by
June.
▴ 10
5
votes
10
replies
545
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2
DGE
contrast
updated 23 months ago by
Michael Love
36k • written 23 months ago by
llooll1
• 0
3
votes
8
replies
511
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 2.4 years ago by
James W. MacDonald
59k • written 2.4 years ago by
s.connell
• 0
0
votes
2
replies
310
views
Longitudinal Time-Course microarray experiment with two time points
edge
DGE
microarray
updated 2.5 years ago by
Gordon Smyth
45k • written 2.5 years ago by
joanasabinopinto
• 0
0
votes
5
replies
442
views
edgeR or DESeq2 between duplicated chromosomes in the same individual
deseq2
edgeR
normalization
DGE
updated 2.6 years ago by
Gordon Smyth
45k • written 2.6 years ago by
grant.dejong
• 0
0
votes
4
replies
1.4k
views
edgeR DGEList and design matrix
edger
DGE
updated 2.8 years ago by
Yunshun Chen
▴ 770 • written 2.8 years ago by
ctstackh
• 0
3
votes
7
replies
640
views
How to determine the cause of no difference between treatments in rnaseq?
RNAseq
DGE
edger
updated 2.9 years ago by
Gordon Smyth
45k • written 2.9 years ago by
jdmontenegroc
• 0
0
votes
0
replies
513
views
quantifying piRNA and tRNA by Salmon
Salmon
DGE
3.5 years ago
lkianmehr
• 0
3
votes
4
replies
1.2k
views
DGE matrix annotation
DGE
DESeq2
AnnotationDbi
updated 3.6 years ago by
James W. MacDonald
59k • written 3.6 years ago by
maxininfa
• 0
0
votes
3
replies
955
views
glmQLFTest, coef=2:4, decideTestDGE not working
edger
DGE
coef
updated 4.6 years ago by
Aaron Lun
★ 27k • written 4.6 years ago by
rebeccajane93
• 0
4
votes
8
replies
1.2k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq
edger
DGE
no replicates
4.8 years ago
Stefany Solano
• 0
5
votes
4
replies
809
views
Experiment design contrasts any time edgeR
DGE
rnaseq
RNA
edger
updated 5.0 years ago by
londonflavido
• 0 • written 5.0 years ago by
Pietro
▴ 30
12
votes
10
replies
4.5k
views
edgeR glmLRT with test="F"?
edger
dge
differential expression
updated 6.9 years ago by
Aaron Lun
★ 27k • written 6.9 years ago by
Ryan C. Thompson
7.8k
16 results • Page
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Comment: EnrichGO not working with db created from annotationhub
by
Lucía
• 0
I have this, can this be used for GO in R? ``` 115709282 LOC115709282 phenylalanine ammonia-lyase 115699364 LOC115699364 …
Answer: EnrichGO not working with db created from annotationhub
by
Lucía
• 0
Hi, thanks so much for all your replies and running the code and confirming. I have not seen any GO term annotations for Cannabis so far…
Comment: TPM data Differential expression analysis
by
Gordon Smyth
45k
I have nothing to add my previous answer, which seems quite clear and umbiguous.
Answer: Difference between raw counts and featureCounts for DESeq2
by
swbarnes2
★ 1.0k
The count output from featureCounts is suitable for use with DESeq.
Comment: Subsetting operation on CompressedGRangesList object 'x' produces a result tha
by
Jiping Wang
▴ 70
Hi H. Do you have any clues what the bug or problem could be? thanks. Jiping
Votes
Answer: Difference between raw counts and featureCounts for DESeq2
Comment: Case Studies Data Missing in Rsubread
Answer: rtracklayer S.h
Answer: rtracklayer S.h
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
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Gordon Smyth
45k
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to
jared.andrews07
▴ 30
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vanbelj
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James W. MacDonald
59k
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Johannes Rainer
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