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4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 11 months ago by
IUH
• 0 • written 6.9 years ago by
stan
• 0
5
votes
9
replies
936
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 21 days ago
Chris
• 0
0
votes
9
replies
849
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
8 months ago
hayleyw
• 0
1
vote
9
replies
5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 6.2 years ago by
klalit1803
• 0
2
votes
9
replies
216
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
2 days ago • updated 3 hours ago
Abbey
• 0
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago • updated 3 months ago
Luca
• 0
1
vote
9
replies
3.0k
views
DEGreport installation help
DEGreport
updated 8 months ago by
James W. MacDonald
65k • written 19 months ago by
marinaw
▴ 20
2
votes
9
replies
3.2k
views
NCBI Locus ID to gene ID conversion
LocusIDtogeneIDconversion
updated 6 months ago by
IP
• 0 • written 20 months ago by
KMS
▴ 20
0
votes
9
replies
567
views
limma fo continous variables
limma
DEGseq
updated 10 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
mia
• 0
0
votes
9
replies
684
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
5 months ago
nromerov
• 0
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler
HPO.db
updated 6 months ago by
Erqiang Hu
▴ 50 • written 6 months ago by
jovel_juan
▴ 30
0
votes
8
replies
1.4k
views
Question about filterByExpr function edgeR
edgeR
8 months ago
lucap
• 0
1
vote
8
replies
1.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression
DESeq2
written 10 months ago by
sean.mccutcheon
• 0
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by
Mingkee
• 0 • written 6.8 years ago by
yura.grabovska
▴ 30
0
votes
8
replies
1.1k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray
TileDBArray
8 months ago • updated 7 months ago
sandmann.t
▴ 70
2
votes
8
replies
548
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
0
votes
8
replies
1.2k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 5 months ago by
yw24418
• 0 • written 14 months ago by
sandra.garces.19
• 0
8
votes
8
replies
9.8k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2
DESeq2
updated 7 months ago by
jd774
• 0 • written 4.8 years ago by
krassowski.michal
▴ 40
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib
rhdf5
3.2 years ago • updated 8 months ago
Thomas Sandmann
▴ 90
0
votes
8
replies
360
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 14 days ago by
swbarnes2
★ 1.3k • written 16 days ago by
Aaliya
• 0
0
votes
8
replies
718
views
Deseq2 Results are different using batch design
DESeq2
9 months ago
hemantcnaik
• 0
3
votes
8
replies
920
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 5 months ago by
pcantalupo
▴ 10
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 5 months ago by
Shaimaa Gamal
• 0 • written 11 months ago by
pg45863
▴ 10
0
votes
8
replies
419
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
9 weeks ago
michelafrancesconi8
• 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge
beta
DESeq2
11 months ago
Ndimensional
▴ 20
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago
Luis
• 0
3
votes
8
replies
530
views
Downloading package mixOmics
mixOmics
11 weeks ago
noortje_bloem94
• 0
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by
Charles Plessy
▴ 180 • written 17 months ago by
Meng
▴ 30
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by
serpalma.v
▴ 60
2
votes
8
replies
1.3k
views
Reading GFF file and pre-processing, run iinfer_syntenet(), input and output
syntenet
updated 4 months ago by
Sujeevan
• 0 • written 16 months ago by
lwanderson8c
• 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
3
votes
8
replies
527
views
Constrast for Time Course Experiments using Limma
limma
9 weeks ago
dl17032000
• 0
1
vote
8
replies
552
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
sat
• 0
0
votes
8
replies
8.6k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 5 months ago by
Marcel Ramos
690 • written 2.8 years ago by
charlotte
▴ 10
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago
Habil Zare
▴ 200
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 16 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
0
votes
8
replies
1.7k
views
flowset/ncdfFlowset replace keywords doesn't work right
ncdfFlow
flowCore
updated 7 months ago by
osayou
• 0 • written 3.6 years ago by
anders.tondell
▴ 30
1
vote
8
replies
1.3k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 5 weeks ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
0
votes
8
replies
826
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression
DESeq2
6 months ago
Luca
• 0
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2
RNASeq
updated 4 months ago by
Jon
• 0 • written 3.4 years ago by
Archit
▴ 10
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
1
vote
8
replies
1.5k
views
News:
Final List of Deprecated Package Bioc 3.9
deprecation
release
software
experimentData
News
written 5.1 years ago by
shepherl
3.9k
0
votes
8
replies
715
views
GOslim missing GO term
GO.db
GOslim
5 months ago
amanda
• 0
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing
RNASeq
IsoformSwitchAnalyzeR
gtf
written 21 months ago by
bpshtiwan
▴ 10
0
votes
8
replies
652
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago
Marianna
▴ 20
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 10 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 22 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
0
votes
7
replies
326
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
22 days ago • updated 16 days ago
hortense96
• 0
1,745 results • Page
3 of 35
Recent ...
Replies
Comment: deseq2 results
by
swbarnes2
★ 1.3k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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