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15
votes
22
replies
1.8k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 5 days ago
Chris
• 0
12
votes
12
replies
761
views
Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by
Robert Castelo
★ 3.3k • written 5 days ago by
Chris
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 6 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 6 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 3 days ago
shepherl
3.8k
6
votes
5
replies
398
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 2 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
4
votes
6
replies
327
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago
Jonathan
▴ 10
4
votes
8
replies
341
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 6 days ago by
Peter Hickey
▴ 740 • written 14 days ago by
Juan Higareda
• 0
3
votes
1
reply
175
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
3
votes
3
replies
284
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 17 days ago by
Netanel
• 0
3
votes
2
replies
155
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 5 days ago by
fernanda.backsouza
▴ 10
3
votes
3
replies
156
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
3
votes
1
reply
117
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
Shaimaa Gamal
• 0
2
votes
4
replies
103
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
1 day ago • updated just now
bandconductor
• 0
2
votes
2
replies
139
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
sansan
• 0
2
votes
5
replies
140
views
get BM error
ensembldb
updated 23 hours ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
2
votes
5
replies
696
views
DESeq2 setting significant p-value
DESeq2
updated 6 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
4
replies
143
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 2 days ago by
James W. MacDonald
65k • written 6 days ago by
Mirella Aurora
• 0
1
vote
4
replies
54
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 28 minutes ago by
James W. MacDonald
65k • written 2 hours ago by
Alexandre
• 0
1
vote
1
reply
70
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
1
vote
13
replies
245
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 18 hours ago
fernanda.backsouza
▴ 10
1
vote
0
replies
199
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
6 days ago • updated 5 days ago
BioinfGuru
▴ 30
1
vote
1
reply
55
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
fernanda.backsouza
▴ 10
1
vote
2
replies
180
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
7 days ago • updated 6 days ago
Le
• 0
1
vote
2
replies
78
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 day ago • updated 7 hours ago
ATpoint
★ 4.0k
1
vote
2
replies
925
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 2 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
220
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
1
vote
3
replies
84
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
1
vote
3
replies
811
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 1 day ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
129
views
minfi::read.metharray.exp
minfiData
minfi
updated 1 day ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 0
0
votes
1
reply
71
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 18 hours ago by
Michael Love
41k • written 21 hours ago by
kcarey
• 0
0
votes
8
replies
223
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 9 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
0
votes
2
replies
106
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
2 days ago • updated 9 hours ago
shuwangxinze1996
• 0
0
votes
0
replies
21
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
7 hours ago
glaciya2018
• 0
0
votes
3
replies
104
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 2 hours ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
0
votes
1
reply
34
views
PCA plot suggestions
DESeq2
PCAtools
updated 1 hour ago by
JKim
• 0 • written 11 hours ago by
Aaliya
• 0
0
votes
0
replies
41
views
Improving the design matrices vignette in RNAseq123
RNAseq123
3 days ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
97
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
ussarizona
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
0
votes
1
reply
89
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
118
views
Adding columns to DEXSeqResults object
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Clyde
• 0
0
votes
1
reply
83
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Alessia
• 0
0
votes
0
replies
87
views
Warning while loading DEP package
DEP
updated 6 days ago by
shepherl
3.8k • written 6 days ago by
Namrata
• 0
0
votes
3
replies
222
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 days ago by
W. Evan Johnson
▴ 850 • written 13 days ago by
schlumbohm
• 0
0
votes
4
replies
131
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago
sropri
• 0
0
votes
2
replies
898
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
6 days ago
prity6459
• 0
72 results • Page
1 of 2
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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