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0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago
kcarey
• 0
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Dev
• 0
0
votes
1
reply
58
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
7 hours ago
minardsmitha
▴ 10
4
votes
6
replies
479
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 29 days ago
Jonathan
▴ 10
0
votes
1
reply
141
views
FDR via q-value
qvalue
updated 29 days ago by
James W. MacDonald
66k • written 4 weeks ago by
John
• 0
0
votes
3
replies
193
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 21 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
0
votes
7
replies
370
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 28 days ago
hortense96
• 0
0
votes
2
replies
173
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
21 days ago • updated 18 days ago
Aurora
• 0
3
votes
5
replies
307
views
Help with running egsea()
EGSEA
15 days ago • updated 13 days ago
Chris
▴ 10
1
vote
4
replies
234
views
minfi::read.metharray.exp
minfiData
minfi
updated 27 days ago by
Basti
▴ 780 • written 29 days ago by
clacarion
• 0
4
votes
2
replies
643
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
19 days ago • updated 15 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
128
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 21 days ago by
shepherl
3.9k • written 21 days ago by
bounlu
• 0
0
votes
4
replies
381
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 10 days ago by
Ziliang
• 0 • written 20 days ago by
Ian D.
▴ 70
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 28 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
1
vote
1
reply
168
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 1 day ago by
James W. MacDonald
66k • written 1 day ago by
ttt
• 0
1
vote
1
reply
68
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 1 day ago by
James W. MacDonald
66k • written 1 day ago by
Đình Vinh
• 0
3
votes
1
reply
330
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 27 days ago by
Michael Love
42k • written 28 days ago by
i.sudbery
▴ 40
0
votes
2
replies
230
views
PCA plot suggestions
DESeq2
PCAtools
updated 25 days ago by
Michael Love
42k • written 26 days ago by
Aaliya
• 0
0
votes
2
replies
69
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
written 1 day ago by
landenshanie
▴ 40
0
votes
1
reply
175
views
ATACseq merge peaks
DiffBind
updated 25 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Shloka
• 0
2
votes
2
replies
240
views
fgsea significant result
fgsea
17 days ago • updated 16 days ago
Chris
▴ 10
2
votes
3
replies
153
views
Problem installing ChAMP on a MacBook
ChAMP
updated 5 days ago by
shepherl
3.9k • written 5 days ago by
Galia
• 0
1
vote
3
replies
265
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
Ashley
• 0
0
votes
3
replies
238
views
Couldn't connect to server while using "pathways"
graphite
updated 15 days ago by
Michael Love
42k • written 15 days ago by
fduguchunhui
• 0
0
votes
1
reply
69
views
ERROR; return code from pthread_create() is 22
affy
updated 1 day ago by
James W. MacDonald
66k • written 3 days ago by
pickingastar
• 0
0
votes
2
replies
135
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
5 days ago
makala
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 15 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
3
votes
4
replies
271
views
Help with error using camera() in limma
CAMERA
limma
21 days ago
Chris
▴ 10
2
votes
9
replies
431
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 26 days ago by
James W. MacDonald
66k • written 26 days ago by
Alexandre
• 0
0
votes
4
replies
267
views
Minfi - estimatecellscount
min
minfi
updated 22 days ago by
James W. MacDonald
66k • written 7 weeks ago by
clacarion
• 0
1
vote
2
replies
125
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
6 days ago
Patadù
▴ 10
2
votes
5
replies
244
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
6 days ago • updated 4 days ago
Patadù
▴ 10
1
vote
3
replies
311
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 20 days ago by
angelathuynh5
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 11 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
1
vote
2
replies
758
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago
Patadù
▴ 10
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 21 days ago
Chris
▴ 10
0
votes
2
replies
72
views
How to run allelic imbalance in apeglm
apeglm
updated 1 day ago by
Michael Love
42k • written 2 days ago by
euge.eugenio
▴ 20
0
votes
5
replies
158
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
2 days ago • updated 1 day ago
Galina
• 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 28 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
149
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
7 days ago • updated 6 days ago
Daniel
• 0
1
vote
1
reply
137
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 28 days ago by
James W. MacDonald
66k • written 28 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
169
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 8 days ago by
Guido Hooiveld
★ 4.0k • written 9 days ago by
aogunbaw
• 0
1
vote
3
replies
113
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by
James W. MacDonald
66k • written 2 days ago by
boczniak767
▴ 720
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 29 days ago by
taur.vil
• 0
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 19 days ago by
Gordon Smyth
50k • written 19 days ago by
z_bahari
• 0
1
vote
2
replies
392
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 18 days ago
Kim
• 0
0
votes
6
replies
563
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 1 day ago
Ken C
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 21 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
1
vote
4
replies
362
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
27 days ago • updated 25 days ago
winwater0928
• 0
0
votes
3
replies
307
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by
Michael Love
42k • written 21 days ago by
HAK
• 0
178 results • Page
2 of 4
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Thank you so much!
Answer: recount3 problem downloading data from source sra
by
Leonardo Collado Torres
★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
minardsmitha
▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
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