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News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
25 days ago
Wolfgang Huber
★ 13k
0
votes
2
replies
164
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
joshua.mannheimer
• 0
0
votes
1
reply
179
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 25 days ago by
James W. MacDonald
65k • written 26 days ago by
BCS12
• 0
0
votes
0
replies
63
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
4 days ago
Chris
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
0
replies
78
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
9 days ago
Dario Strbenac
★ 1.5k
0
votes
1
reply
119
views
what is the sampleFiles
chipseq
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
zhulin
• 0
0
votes
1
reply
77
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
z_bahari
• 0
0
votes
0
replies
80
views
Enzyme Engineering
BioTIP
16 days ago
bocchemistry
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 20 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
131
views
Bioinformatics student
Des
DESeq2
updated 21 days ago by
hemantcnaik
• 0 • written 21 days ago by
Sahar
• 0
0
votes
1
reply
141
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
quanah.hudson
• 0
0
votes
3
replies
146
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
bas_work
▴ 30
0
votes
1
reply
142
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 9 days ago by
Michael Love
41k • written 9 days ago by
kcarey
• 0
0
votes
2
replies
205
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
14 days ago • updated 11 days ago
catv
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
4
replies
595
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 17 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
2
replies
191
views
PCA plot suggestions
DESeq2
PCAtools
updated 7 days ago by
Michael Love
41k • written 9 days ago by
Aaliya
• 0
0
votes
4
replies
5.5k
views
SingleR Label.Ont
SingleR
updated 18 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
0
replies
142
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
25 days ago
arne.sahm
• 0
0
votes
0
replies
143
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
28 days ago
andromeda
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 12 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
1
reply
151
views
Adding columns to DEXSeqResults object
DEXSeq
updated 15 days ago by
Alejandro Reyes
★ 1.9k • written 17 days ago by
Clyde
• 0
0
votes
0
replies
68
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
10 days ago
info
▴ 10
0
votes
1
reply
115
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
angelathuynh5
• 0
0
votes
0
replies
102
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
9 days ago • updated 23 hours ago
glaciya2018
• 0
0
votes
3
replies
251
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 15 days ago by
W. Evan Johnson
▴ 850 • written 21 days ago by
schlumbohm
• 0
0
votes
1
reply
338
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 23 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
0
votes
3
replies
110
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
james.zhang20
• 0
0
votes
0
replies
82
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
21 days ago
shepherl
3.9k
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
23 days ago
Dennis
• 0
0
votes
2
replies
105
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
2 days ago • updated 1 day ago
Ian D.
▴ 70
0
votes
1
reply
109
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 15 days ago by
Michael Love
41k • written 15 days ago by
09191919
• 0
0
votes
4
replies
306
views
Help with design.matrix
limma
28 days ago • updated 27 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
166
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
gene_bioconductor
▴ 10
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 3 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 days ago
Virangika
• 0
0
votes
7
replies
304
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
16 days ago • updated 10 days ago
hortense96
• 0
0
votes
2
replies
240
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
11 days ago • updated 9 days ago
shuwangxinze1996
• 0
0
votes
0
replies
26
views
Handling multiple differential expression comparisons
DESeq2
14 hours ago
Zainab
• 0
0
votes
5
replies
290
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 9 days ago by
James W. MacDonald
65k • written 12 days ago by
Gayatri
• 0
0
votes
2
replies
105
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
4 days ago • updated 22 hours ago
Aurora
• 0
0
votes
3
replies
130
views
Store output of matchPWM()
biostrings
Biostrings
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
mat149
▴ 70
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
22 days ago
Stevie Pederson
• 0
0
votes
3
replies
222
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 3 days ago by
James W. MacDonald
65k • written 4 days ago by
SSSJec
• 0
0
votes
1
reply
214
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 3 days ago by
James W. MacDonald
65k • written 4 days ago by
SSSJec
• 0
0
votes
6
replies
140
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 2 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
arfranco
▴ 130
0
votes
0
replies
50
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
3 days ago
Maria Doyle
▴ 70
0
votes
1
reply
93
views
putting my own expression data in deseq2
DESeq2
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
Dev
• 0
0
votes
0
replies
68
views
Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 11 hours ago
Chris
• 0
202 results • Page
3 of 5
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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