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12
votes
13
replies
828
views
Why p value inconsistent when using different number of pathway score?
limma
7 days ago • updated 2 hours ago
Chris
• 0
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 5 days ago
shepherl
3.8k
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 4 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 4 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
4
votes
6
replies
357
views
FilterByExpr low counts with small sample size
edgeR
10 days ago • updated 5 days ago
Jonathan
▴ 10
3
votes
3
replies
179
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
WardDeb
• 0
3
votes
3
replies
295
views
permutation test in edgeR
rna-seq
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 19 days ago by
Netanel
• 0
3
votes
1
reply
236
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
i.sudbery
▴ 40
3
votes
2
replies
171
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 8 days ago by
fernanda.backsouza
▴ 10
2
votes
5
replies
170
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 2 days ago by
James W. MacDonald
65k • written 4 days ago by
bandconductor
• 0
2
votes
5
replies
176
views
get BM error
ensembldb
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
Fara
• 0
2
votes
9
replies
281
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
Alexandre
• 0
1
vote
3
replies
138
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
100
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
3 days ago • updated 2 days ago
ATpoint
★ 4.0k
1
vote
4
replies
167
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 5 days ago by
James W. MacDonald
65k • written 9 days ago by
Mirella Aurora
• 0
1
vote
1
reply
106
views
Citation for edgeR user guide
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
k___
▴ 30
1
vote
1
reply
72
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
fernanda.backsouza
▴ 10
1
vote
4
replies
209
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
3 days ago • updated 1 day ago
winwater0928
• 0
1
vote
1
reply
63
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 23 hours ago by
Leo Lahti
▴ 40 • written 1 day ago by
Dario Strbenac
★ 1.5k
1
vote
13
replies
307
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
6 days ago • updated 3 days ago
fernanda.backsouza
▴ 10
1
vote
3
replies
124
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 day ago by
Michael Love
41k • written 2 days ago by
JalapenoCornbread
• 0
1
vote
2
replies
398
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago
ussarizona
▴ 10
1
vote
4
replies
154
views
minfi::read.metharray.exp
minfiData
minfi
updated 3 days ago by
Basti
▴ 780 • written 5 days ago by
clacarion
• 0
1
vote
7
replies
186
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
2 days ago • updated 1 day ago
pl23
• 0
1
vote
2
replies
937
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 4 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
3
replies
822
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 3 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
101
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 1 day ago by
Gordon Smyth
50k • written 5 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
64
views
ATACseq merge peaks
DiffBind
updated 1 day ago by
ATpoint
★ 4.0k • written 3 days ago by
Shloka
• 0
0
votes
2
replies
117
views
PCA plot suggestions
DESeq2
PCAtools
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Aaliya
• 0
0
votes
7
replies
260
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
10 days ago • updated 4 days ago
hortense96
• 0
0
votes
1
reply
103
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
taur.vil
• 0
0
votes
1
reply
90
views
FDR via q-value
qvalue
updated 5 days ago by
James W. MacDonald
65k • written 8 days ago by
John
• 0
0
votes
0
replies
34
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
4 days ago
info
▴ 10
0
votes
7
replies
638
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 4 days ago
shepherl
3.8k
0
votes
2
replies
164
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
8 days ago • updated 5 days ago
catv
• 0
0
votes
0
replies
40
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
3 days ago
Dario Strbenac
★ 1.5k
0
votes
5
replies
243
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 3 days ago by
James W. MacDonald
65k • written 6 days ago by
Gayatri
• 0
0
votes
0
replies
32
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
3 days ago
Sara
• 0
0
votes
1
reply
88
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 3 days ago by
Michael Love
41k • written 3 days ago by
kcarey
• 0
0
votes
8
replies
260
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 2 days ago by
swbarnes2
★ 1.3k • written 4 days ago by
Aaliya
• 0
0
votes
2
replies
159
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
4 days ago • updated 2 days ago
shuwangxinze1996
• 0
0
votes
0
replies
40
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
2 days ago
glaciya2018
• 0
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 5 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
47
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
6 days ago
vaxahey107
• 0
44 results • Page
1 of 1
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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