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Showing :
paired
•
reset
0
votes
0
replies
374
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
11 months ago
julie.chevalier
• 0
1
vote
6
replies
1.2k
views
DESeq2 design for paired samples
DESeq2
paired
updated 2.8 years ago by
Michael Love
42k • written 2.8 years ago by
annamariabugaj
▴ 10
0
votes
1
reply
973
views
Subject paired DESeq2 design
DESeq2
paired
design
updated 2.9 years ago by
Michael Love
42k • written 2.9 years ago by
dr
▴ 10
1
vote
15
replies
2.6k
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
3.2 years ago
demisa
• 0
0
votes
0
replies
553
views
PROPER for paired samples
PROPER
Paired
3.9 years ago
christoph8
• 0
2
votes
6
replies
1.4k
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 4.1 years ago by
Gordon Smyth
51k • written 4.1 years ago by
ScA
• 0
1
vote
1
reply
616
views
DESeq2 paired test (for most samples)
deseq2
paired
tumor vs normal
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
dagsbio
• 0
1
vote
2
replies
820
views
Correct DESeq2 interaction design and results with paired and nested data
deseq2
Paired
Nested
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
julia.chariker
▴ 10
0
votes
1
reply
1.5k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2
comparison
design
paired
treatment
updated 4.6 years ago by
swbarnes2
★ 1.4k • written 4.6 years ago by
tinglec
• 0
1
vote
3
replies
1.1k
views
How can I run a paired RankProd analysis in R?
RankProd
paired
RNAseq
R
updated 4.6 years ago by
James W. MacDonald
66k • written 4.6 years ago by
joker33
• 0
1
vote
2
replies
1.6k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma
microarray
time series
DEG
paired
updated 4.7 years ago by
Gordon Smyth
51k • written 4.7 years ago by
kawess
• 0
6
votes
6
replies
1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 4.8 years ago by
Gordon Smyth
51k • written 4.8 years ago by
english.server
▴ 20
3
votes
3
replies
905
views
Paired design in limma
limma
paired
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
rasmus.agren
• 0
0
votes
1
reply
664
views
Paired samples in DESeq2
R
deseq2
Paired
Samples
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
m.wekking
• 0
3
votes
6
replies
2.8k
views
Limma design/contrast correct?
limma
microarray
design
paired
mixed model
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
rasmus.agren
• 0
4
votes
9
replies
1.6k
views
limma paired design with continous covariate
limma
paired
covariate
updated 8.1 years ago by
Steve Lianoglou
★ 13k • written 8.1 years ago by
meeta.mistry
▴ 30
3
votes
3
replies
2.0k
views
read counts of paired end reads for DESeq2 analysis
deseq
featurecounts
paired
updated 8.1 years ago by
Steve Lianoglou
★ 13k • written 8.1 years ago by
tszn1984
• 0
1
vote
5
replies
1.8k
views
diffHic preparePairs() does not identify paired-end reads
diffHic
preparePairs
paired
BAM
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
ilyco
• 0
1
vote
9
replies
3.7k
views
LIMMA for paired analysis with adjustment for confounding continuous variables
limma
gene expression
confounding
adjustment
paired
8.6 years ago
Loodramon
• 0
0
votes
2
replies
1.3k
views
Using merged alignments of PE readlists for DEXSeq
dexseq
paired
rnaseq
samtools merge
updated 8.8 years ago by
Alejandro Reyes
★ 1.9k • written 8.8 years ago by
arom2
• 0
0
votes
1
reply
1.2k
views
WGCNA package with monozygotic twin data
wgcna
Twin Analysis
within-pair analysis
paired
updated 9.1 years ago by
Peter Langfelder
★ 3.0k • written 9.1 years ago by
mahes.muniandy
• 0
4
votes
7
replies
3.4k
views
Correct implementation of multifactorial paired analysis in limma software package for DE expression
limma
microarray
multiple factor design
paired
updated 9.3 years ago by
Gordon Smyth
51k • written 9.3 years ago by
svlachavas
▴ 830
2
votes
1
reply
1.6k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired
batcheffect
updated 9.4 years ago by
Gordon Smyth
51k • written 9.4 years ago by
cinderelliedoll
• 0
4
votes
14
replies
5.5k
views
Including technical and biological replicates in Limma block analysis?
limma
microarray
block
paired
linear model
9.5 years ago
vas
▴ 40
7
votes
15
replies
16k
views
DESeq2 paired multifactor test
deseq2
paired
updated 18 months ago by
teabonng
• 0 • written 9.6 years ago by
hwillenbrock
▴ 20
1
vote
6
replies
3.5k
views
Limma: advice needed for best approach for joint paired and unpaired analyses in unbalanced intervention study
limma
paired
unpaired
duplicateCorrelation
updated 9.6 years ago by
bcbio_uk
▴ 10 • written 9.6 years ago by
Guido Hooiveld
★ 4.0k
1
vote
5
replies
2.0k
views
limma paired design matrix 3 factors
limma
paired
design and contrast matrix
9.7 years ago • updated 9.6 years ago
wim.trypsteen
• 0
27 results • Page
1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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Jonathan
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