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Showing :
Paired
•
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0
votes
0
replies
385
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
12 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
989
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
563
views
PROPER for paired samples
PROPER
Paired
3.9 years ago
christoph8
• 0
2
votes
6
replies
1.5k
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
628
views
DESeq2 paired test (for most samples)
deseq2
paired
tumor vs normal
updated 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
dagsbio
• 0
1
vote
2
replies
836
views
Correct DESeq2 interaction design and results with paired and nested data
deseq2
Paired
Nested
updated 4.5 years ago by
Michael Love
42k • written 4.5 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 4.7 years ago by
James W. MacDonald
66k • written 4.7 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 4.8 years ago by
Gordon Smyth
51k • written 4.8 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
913
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
674
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 8.2 years ago by
Steve Lianoglou
★ 13k • written 8.2 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 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 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
8.7 years ago
Loodramon
• 0
0
votes
2
replies
1.4k
views
Using merged alignments of PE readlists for DEXSeq
dexseq
paired
rnaseq
samtools merge
updated 8.9 years ago by
Alejandro Reyes
★ 1.9k • written 8.9 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 9.4 years ago by
Gordon Smyth
51k • written 9.4 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
5.6k
views
Including technical and biological replicates in Limma block analysis?
limma
microarray
block
paired
linear model
9.6 years ago
vas
▴ 40
7
votes
15
replies
16k
views
DESeq2 paired multifactor test
deseq2
paired
updated 19 months ago by
teabonng
• 0 • written 9.7 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 9.7 years ago by
bcbio_uk
▴ 10 • written 9.7 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
wim.trypsteen
• 0
27 results • Page
1 of 1
Recent ...
Replies
Comment: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data
by
Elodie
• 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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