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10
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Help with error using camera() in limma
CAMERA
18 minutes ago
Chris
• 0
0
votes
1
reply
29
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 hour ago by
Michael Love
41k • written 2 hours ago by
marcusn
• 0
0
votes
1
reply
32
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 hour ago by
Michael Love
41k • written 7 hours ago by
Aurora
• 0
0
votes
1
reply
33
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 hour ago by
Michael Love
41k • written 19 hours ago by
Agung
• 0
0
votes
0
replies
11
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
2 hours ago
Maria Doyle
▴ 70
0
votes
1
reply
29
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 hours ago by
shepherl
3.8k • written 10 hours ago by
bounlu
• 0
0
votes
1
reply
32
views
putting my own expression data in deseq2
DESeq2
updated 4 hours ago by
ATpoint
★ 4.1k • written 5 hours ago by
Dev
• 0
0
votes
0
replies
11
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
12 hours ago
SSSJec
• 0
2
votes
2
replies
121
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
20 hours ago • updated 19 hours ago
Chris
• 0
0
votes
2
replies
125
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
1 day ago • updated 12 hours ago
SSSJec
• 0
0
votes
0
replies
32
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
1 day ago • updated 22 hours ago
Chris
• 0
3
votes
3
replies
161
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
bioinf
▴ 10
1
vote
1
reply
93
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 3 days ago by
Leo Lahti
▴ 40 • written 4 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
156
views
PCA plot suggestions
DESeq2
PCAtools
updated 3 days ago by
Michael Love
41k • written 5 days ago by
Aaliya
• 0
1
vote
3
replies
164
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 4 days ago by
Michael Love
41k • written 4 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
95
views
ATACseq merge peaks
DiffBind
updated 4 days ago by
ATpoint
★ 4.1k • written 5 days ago by
Shloka
• 0
1
vote
1
reply
135
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 4 days ago by
Gordon Smyth
50k • written 8 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
252
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
4 days ago • updated 3 days ago
pl23
• 0
2
votes
9
replies
321
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
Alexandre
• 0
0
votes
0
replies
61
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
5 days ago
glaciya2018
• 0
1
vote
2
replies
125
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
6 days ago • updated 5 days ago
ATpoint
★ 4.1k
0
votes
1
reply
114
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 5 days ago by
Michael Love
41k • written 5 days ago by
kcarey
• 0
0
votes
0
replies
58
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
6 days ago • updated 1 day ago
Sara
• 0
2
votes
5
replies
223
views
get BM error
ensembldb
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
Fara
• 0
2
votes
5
replies
201
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 4 days ago by
James W. MacDonald
65k • written 6 days ago by
bandconductor
• 0
0
votes
0
replies
61
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
6 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
185
views
Different Shrunk Log2FC according with reference
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
272
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
6 days ago • updated 4 days ago
winwater0928
• 0
3
votes
1
reply
277
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
i.sudbery
▴ 40
1
vote
1
reply
145
views
Citation for edgeR user guide
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
k___
▴ 30
0
votes
7
replies
667
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 6 days ago
shepherl
3.8k
1
vote
1
reply
90
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
304
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 5 days ago by
swbarnes2
★ 1.3k • written 6 days ago by
Aaliya
• 0
0
votes
0
replies
49
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
7 days ago
info
▴ 10
1
vote
4
replies
180
views
minfi::read.metharray.exp
minfiData
minfi
updated 6 days ago by
Basti
▴ 780 • written 7 days ago by
clacarion
• 0
0
votes
2
replies
204
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
7 days ago • updated 5 days ago
shuwangxinze1996
• 0
1
vote
2
replies
959
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 7 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
121
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
taur.vil
• 0
3
votes
3
replies
200
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
WardDeb
• 0
1
vote
4
replies
191
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 7 days ago by
James W. MacDonald
65k • written 11 days ago by
Mirella Aurora
• 0
0
votes
1
reply
108
views
FDR via q-value
qvalue
updated 8 days ago by
James W. MacDonald
65k • written 10 days ago by
John
• 0
0
votes
5
replies
276
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 6 days ago by
James W. MacDonald
65k • written 8 days ago by
Gayatri
• 0
0
votes
2
replies
181
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
11 days ago • updated 8 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 8 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 8 days ago
shepherl
3.8k
1
vote
13
replies
350
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
8 days ago • updated 5 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
68
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
9 days ago
vaxahey107
• 0
14
votes
17
replies
1.0k
views
Why p value inconsistent when using different number of pathway score?
limma
10 days ago • updated 1 hour ago
Chris
• 0
0
votes
0
replies
85
views
I am trying to detect alternative splicing.
ASpli
10 days ago
Sebashish
• 0
3
votes
2
replies
192
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 8 days ago by
Guido Hooiveld
★ 3.9k • written 10 days ago by
fernanda.backsouza
▴ 10
45,593 results • Page
1 of 912
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
Sorry, for questions about statistical analysis plan and interpretation of results, I recommend to work with a local statistician or someon…
Answer: Fold change calculation in Diffbind vs. DESEQ2?
by
Michael Love
41k
There was a recent DiffBind question on the support site that noticed the same thing, try searching recent DiffBind posts.
Answer: Timecourse RNASeq analysis
by
Michael Love
41k
There are many choices for time course, and we have an example in our workflow (rnaseqGene). Otherwise, I recommend to consult a local …
Answer: Padj "NA" with thousands of low count although the raw read counts are quite lar
by
Michael Love
41k
You can either turn off independent filtering in `results` or use `ihw` see the vignette.
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Thanks Gordon for a detail guide! You have a great memory of time. GSVA also do differential express at pathway level (https://bioconductor…
Votes
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
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bioinf
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