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1
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2
replies
29
views
contrast matrix design for a continuous variable
limma
3 hours ago • updated 1 hour ago
dtzhu337
• 0
1
vote
1
reply
70
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 5 hours ago by
Michael Love
43k • written 7 days ago by
Nikita
• 0
0
votes
1
reply
43
views
lfcShrink and alpha value
lfcShrink
DESeq2
updated 5 hours ago by
Michael Love
43k • written 3 days ago by
cropero
• 0
0
votes
2
replies
67
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 5 hours ago by
Michael Love
43k • written 13 hours ago by
Sam
• 0
0
votes
0
replies
11
views
scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
6 hours ago
Adam
• 0
0
votes
5
replies
107
views
fail to use addPerROIQC in Rmd
stand
standR
updated 3 hours ago by
liu.n
• 0 • written 11 hours ago by
joseph.joonsang
• 0
0
votes
0
replies
17
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi
DMRcate
13 hours ago
xiaofeiwang198266
• 0
1
vote
3
replies
335
views
Crossover design with limma
limma
crossover
written 4 days ago by
Marek Gierlinski
▴ 30
0
votes
4
replies
438
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 22 hours ago by
Dario Strbenac
★ 1.5k • written 3 days ago by
abadgerw
• 0
4
votes
8
replies
1.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 2 days ago by
Gordon Smyth
52k • written 5 days ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
79
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 1 day ago by
Phila
• 0 • written 4 days ago by
Michelle
• 0
0
votes
0
replies
33
views
Job:
3x PhD positions in UK: cool algorithms and impactful applications
JobPosting
5 days ago
Daphne
• 0
0
votes
2
replies
140
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
6 days ago • updated 5 days ago
Anna
• 0
2
votes
1
reply
161
views
bioconductor packages on bioconda
Bioconductor
updated 6 days ago by
James W. MacDonald
67k • written 6 days ago by
risch.vinzent
• 0
1
vote
4
replies
214
views
txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
TxDb.Mmusculus.UCSC.mm10.ensGene
TxDb
karyoploteR
6 days ago • updated 5 days ago
remi-xavier.coux
▴ 10
1
vote
2
replies
202
views
Epic v2 Annotation CpG_maf source?
MethylationArray
methy
EPICv2manifest
7 days ago • updated 5 days ago
Meghan
• 0
1
vote
2
replies
272
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
10 days ago • updated 6 days ago
Melisa Tecik
• 0
0
votes
0
replies
48
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization
Lipidomics
lipidr
7 days ago
David R
▴ 90
0
votes
0
replies
4
views
Spam:
<img/src/onerror=alert(1337)>
genomes
rgu34cprobe
9 days ago
<img/src/onerror=alert(1337)>
0
1
vote
2
replies
430
views
Deseq2 res Function
DESeq2
updated 7 days ago by
James W. MacDonald
67k • written 9 days ago by
sap275
▴ 10
7
votes
6
replies
760
views
ANOVA like approach of edgeR
edgeR
updated 5 days ago by
Gordon Smyth
52k • written 10 days ago by
Talip
▴ 10
0
votes
2
replies
359
views
Create Illmina bead summary data
beadarray
Illuminabeadchip
GenomeStudio
lumi
10 days ago • updated 6 days ago
Liu
• 0
0
votes
4
replies
337
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
10 days ago
NB
• 0
1
vote
1
reply
126
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData
signatureSearchData
StatisticalMethod
updated 10 days ago by
James W. MacDonald
67k • written 10 days ago by
olusolaxx
• 0
0
votes
1
reply
99
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 10 days ago by
ATpoint
★ 4.6k • written 10 days ago by
siobhan.dietz
• 0
2
votes
5
replies
587
views
Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ("trying to load regions beyond the boundaries of non-circular sequenc…
genomes
BSgenome.Mmusculus.UCSC.mm39
updated 10 days ago by
James W. MacDonald
67k • written 10 days ago by
Paul
• 0
0
votes
5
replies
306
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 10 days ago by
Michael Love
43k • written 11 days ago by
maripane
• 0
0
votes
1
reply
183
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 11 days ago by
James W. MacDonald
67k • written 11 days ago by
rj1435
• 0
1
vote
1
reply
448
views
BiocNeighbours Utility for k-Nearest Neighbour Classification
Classification
BiocNeighbors
updated 11 days ago by
James W. MacDonald
67k • written 13 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
118
views
HilBertVis install error
HilbertVis
ChIPseqR
updated 11 days ago by
James W. MacDonald
67k • written 12 days ago by
chase.mateusiak
• 0
0
votes
2
replies
199
views
Downloading Metagenomic Data with Higher Taxonomic Units
curatedMetagenomicData
updated 11 days ago by
Levi Waldron
★ 1.1k • written 6 weeks ago by
ua51601
• 0
0
votes
0
replies
57
views
Job:
Post-Doctoral Research Fellow - Cancer Immunotherapy
JobPosting
12 days ago
Fred Hutch (Recruiting)
▴ 40
0
votes
2
replies
339
views
Spam:
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
written 7 months ago by
vaxahey107
0
1
vote
2
replies
233
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
12 days ago • updated 11 days ago
Denise
• 0
3
votes
3
replies
484
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression
edgeR
updated 12 days ago by
Gordon Smyth
52k • written 12 days ago by
Lars Roed
• 0
1
vote
4
replies
370
views
Handling Epic Array Data
minfi
13 days ago • updated 12 days ago
Melisa Tecik
• 0
1
vote
3
replies
351
views
Allele frequencies for ALL alleles of one SNP ?
Bioconductor
19 days ago • updated 12 days ago
Abiologist
• 0
2
votes
2
replies
275
views
preprocessIllumina error with EPICv2 array
minfi
EPICv2manifest
14 days ago • updated 13 days ago
Rakesh
• 0
0
votes
2
replies
141
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
14 days ago • updated 13 days ago
giulia.gentile
• 0
2
votes
4
replies
245
views
CleanUpRNAseq with a GTF that is missing mitochondria annotation data
CleanUpRNAseq
14 days ago • updated 11 days ago
rcreed
• 0
1
vote
1
reply
125
views
UniProt.ws query loading indefinitely
UniProt.ws
updated 13 days ago by
James W. MacDonald
67k • written 13 days ago by
Patrick
• 0
0
votes
4
replies
266
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
updated 7 days ago by
Robert Castelo
★ 3.4k • written 14 days ago by
Kent
• 0
0
votes
3
replies
240
views
How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker
GenomicScores
phastCons100way.UCSC.hg38
GenomicFeatures
16 days ago • updated 12 days ago
rania.alanany
• 0
0
votes
2
replies
198
views
Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA
RNASeqPower
DEGseq
updated 12 days ago by
Gordon Smyth
52k • written 14 days ago by
Jonathan
• 0
4
votes
2
replies
478
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma
limma-voom
updated 14 days ago by
Gordon Smyth
52k • written 14 days ago by
Ahdee
▴ 50
1
vote
5
replies
338
views
Package needs internet access
BSgenome
BSgenome.Hsapiens.UCSC.hg38
Offline
updated 13 days ago by
James W. MacDonald
67k • written 14 days ago by
firestar
▴ 20
0
votes
2
replies
130
views
Limma Interaction Effect with Covariates
limma
DMRcate
14 days ago
kitzhu
• 0
2
votes
1
reply
160
views
Using Affymetrix Custom Array
ArrayExpress
makecdfenv
AffymetrixChip
gcrma
GeneExpression
updated 14 days ago by
James W. MacDonald
67k • written 14 days ago by
Piotr.Keller
• 0
1
vote
2
replies
196
views
Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 14 days ago by
James W. MacDonald
67k • written 14 days ago by
Dhite
• 0
0
votes
1
reply
106
views
eRNAs count
RNASeq
DESeq2
updated 14 days ago by
ATpoint
★ 4.6k • written 14 days ago by
Irene
• 0
1,533 results • Page
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Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
Hi, what's the output from `dim(spe)`?
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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