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Showing :
paired
•
reset
0
votes
0
replies
505
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
18 months ago
julie.chevalier
• 0
1
vote
6
replies
1.4k
views
DESeq2 design for paired samples
DESeq2
paired
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
annamariabugaj
▴ 10
0
votes
1
reply
1.2k
views
Subject paired DESeq2 design
DESeq2
paired
design
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
dr
▴ 10
1
vote
15
replies
3.1k
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
3.7 years ago
demisa
• 0
0
votes
0
replies
687
views
PROPER for paired samples
PROPER
Paired
4.4 years ago
christoph8
• 0
2
votes
6
replies
1.7k
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 4.6 years ago by
Gordon Smyth
52k • written 4.6 years ago by
ScA
• 0
1
vote
1
reply
736
views
DESeq2 paired test (for most samples)
deseq2
paired
tumor vs normal
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
dagsbio
• 0
1
vote
2
replies
987
views
Correct DESeq2 interaction design and results with paired and nested data
deseq2
Paired
Nested
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
julia.chariker
▴ 10
0
votes
1
reply
1.7k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2
comparison
design
paired
treatment
updated 5.1 years ago by
swbarnes2
★ 1.4k • written 5.1 years ago by
tinglec
• 0
1
vote
3
replies
1.2k
views
How can I run a paired RankProd analysis in R?
RankProd
paired
RNAseq
R
updated 5.2 years ago by
James W. MacDonald
67k • written 5.2 years ago by
joker33
• 0
1
vote
2
replies
2.0k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma
microarray
time series
DEG
paired
updated 5.2 years ago by
Gordon Smyth
52k • written 5.2 years ago by
kawess
• 0
6
votes
6
replies
1.9k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma
paired
batch
updated 5.3 years ago by
Gordon Smyth
52k • written 5.3 years ago by
english.server
▴ 20
3
votes
3
replies
1.0k
views
Paired design in limma
limma
paired
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
rasmus.agren
• 0
0
votes
1
reply
756
views
Paired samples in DESeq2
R
deseq2
Paired
Samples
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
m.wekking
• 0
3
votes
6
replies
3.2k
views
Limma design/contrast correct?
limma
microarray
design
paired
mixed model
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
rasmus.agren
• 0
4
votes
9
replies
1.8k
views
limma paired design with continous covariate
limma
paired
covariate
updated 8.6 years ago by
Steve Lianoglou
★ 13k • written 8.6 years ago by
meeta.mistry
▴ 30
3
votes
3
replies
2.1k
views
read counts of paired end reads for DESeq2 analysis
deseq
featurecounts
paired
updated 8.7 years ago by
Steve Lianoglou
★ 13k • written 8.7 years ago by
tszn1984
• 0
1
vote
5
replies
1.9k
views
diffHic preparePairs() does not identify paired-end reads
diffHic
preparePairs
paired
BAM
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
ilyco
• 0
1
vote
9
replies
4.0k
views
LIMMA for paired analysis with adjustment for confounding continuous variables
limma
gene expression
confounding
adjustment
paired
9.1 years ago
Loodramon
• 0
0
votes
2
replies
1.5k
views
Using merged alignments of PE readlists for DEXSeq
dexseq
paired
rnaseq
samtools merge
updated 9.3 years ago by
Alejandro Reyes
★ 1.9k • written 9.3 years ago by
arom2
• 0
0
votes
1
reply
1.3k
views
WGCNA package with monozygotic twin data
wgcna
Twin Analysis
within-pair analysis
paired
updated 9.6 years ago by
Peter Langfelder
★ 3.0k • written 9.6 years ago by
mahes.muniandy
• 0
4
votes
7
replies
3.5k
views
Correct implementation of multifactorial paired analysis in limma software package for DE expression
limma
microarray
multiple factor design
paired
updated 9.8 years ago by
Gordon Smyth
52k • written 9.9 years ago by
svlachavas
▴ 840
2
votes
1
reply
1.7k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired
batcheffect
updated 9.9 years ago by
Gordon Smyth
52k • written 9.9 years ago by
cinderelliedoll
• 0
4
votes
14
replies
5.9k
views
Including technical and biological replicates in Limma block analysis?
limma
microarray
block
paired
linear model
10.0 years ago
vas
▴ 40
7
votes
15
replies
16k
views
DESeq2 paired multifactor test
deseq2
paired
updated 2.0 years ago by
teabonng
• 0 • written 10.2 years ago by
hwillenbrock
▴ 20
1
vote
6
replies
3.7k
views
Limma: advice needed for best approach for joint paired and unpaired analyses in unbalanced intervention study
limma
paired
unpaired
duplicateCorrelation
updated 10.1 years ago by
bcbio_uk
▴ 10 • written 10.2 years ago by
Guido Hooiveld
★ 4.1k
1
vote
5
replies
2.2k
views
limma paired design matrix 3 factors
limma
paired
design and contrast matrix
10.2 years ago
wim.trypsteen
• 0
27 results • Page
1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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