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5
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
26 minutes ago
pl23
• 0
2
votes
6
replies
85
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 40 minutes ago by
SamGG
▴ 350 • written 5 hours ago by
Alexandre
• 0
0
votes
0
replies
24
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
10 hours ago
glaciya2018
• 0
0
votes
1
reply
45
views
PCA plot suggestions
DESeq2
PCAtools
updated 3 hours ago by
JKim
• 0 • written 14 hours ago by
Aaliya
• 0
0
votes
1
reply
73
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 21 hours ago by
Michael Love
41k • written 1 day ago by
kcarey
• 0
0
votes
0
replies
21
views
ATACseq merge peaks
DiffBind
1 day ago
Shloka
• 0
0
votes
0
replies
17
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
1 day ago
Sara
• 0
0
votes
0
replies
27
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
1 day ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
81
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 day ago • updated 10 hours ago
ATpoint
★ 4.0k
1
vote
3
replies
90
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
3
replies
109
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 4 hours ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
2
votes
5
replies
141
views
get BM error
ensembldb
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
2
votes
5
replies
126
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 1 hour ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
1
vote
1
reply
72
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
3
votes
1
reply
197
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
1
vote
1
reply
58
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
228
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 12 hours ago by
swbarnes2
★ 1.3k • written 2 days ago by
Aaliya
• 0
0
votes
0
replies
26
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
2 days ago
info
▴ 10
0
votes
2
replies
109
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 12 hours ago
shuwangxinze1996
• 0
0
votes
1
reply
89
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
taur.vil
• 0
3
votes
3
replies
157
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
WardDeb
• 0
1
vote
4
replies
129
views
minfi::read.metharray.exp
minfiData
minfi
updated 1 day ago by
Basti
▴ 780 • written 3 days ago by
clacarion
• 0
0
votes
0
replies
45
views
Improving the design matrices vignette in RNAseq123
RNAseq123
3 days ago
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
211
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 1 day ago by
James W. MacDonald
65k • written 3 days ago by
Gayatri
• 0
1
vote
13
replies
254
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
4 days ago • updated 21 hours ago
fernanda.backsouza
▴ 10
0
votes
0
replies
40
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
4 days ago
vaxahey107
• 0
12
votes
12
replies
764
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
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
5 days ago
Sebashish
• 0
3
votes
2
replies
158
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
0
votes
1
reply
81
views
FDR via q-value
qvalue
updated 3 days ago by
James W. MacDonald
65k • written 6 days ago by
John
• 0
0
votes
2
replies
152
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
6 days ago • updated 3 days ago
catv
• 0
0
votes
3
replies
102
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
bas_work
▴ 30
1
vote
0
replies
202
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
6 days ago
BioinfGuru
▴ 30
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
6 days ago
prity6459
• 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
0
votes
4
replies
132
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago
sropri
• 0
1
vote
4
replies
145
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 3 days ago by
James W. MacDonald
65k • written 7 days ago by
Mirella Aurora
• 0
0
votes
3
replies
129
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
prity6459
• 0
0
votes
0
replies
87
views
Warning while loading DEP package
DEP
updated 7 days ago by
shepherl
3.8k • written 7 days ago by
Namrata
• 0
0
votes
1
reply
83
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Alessia
• 0
0
votes
1
reply
89
views
rlog transformation
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 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
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
124
views
Error in champ.load(): The following specified files do not exist
ChAMP
7 days ago
Sherin
• 0
0
votes
1
reply
78
views
Input Question for deseq.r
RSeqAn
updated 7 days ago by
ATpoint
★ 4.0k • written 7 days ago by
Nina
• 0
4
votes
6
replies
328
views
FilterByExpr low counts with small sample size
edgeR
8 days ago • updated 3 days ago
Jonathan
▴ 10
0
votes
4
replies
198
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
8 days ago • updated 5 days ago
lonn
• 0
0
votes
1
reply
97
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
ussarizona
• 0
0
votes
1
reply
116
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by
ATpoint
★ 4.0k • written 8 days ago by
quanah.hudson
• 0
45,579 results • Page
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
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…
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Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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
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