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Views
Votes
2
votes
6
replies
1.6k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
21 months ago
Lily Cheang
▴ 10
3
votes
8
replies
1.4k
views
Constrast for Time Course Experiments using Limma
limma
21 months ago
dl17032000
• 0
1
vote
4
replies
932
views
DESeq2 Replicates
DESeq2
RNASeq
21 months ago
kcarey
• 0
2
votes
6
replies
1.0k
views
Factor vs Character in design
DESeq2
21 months ago
James Aiden
• 0
1
vote
3
replies
1.1k
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
21 months ago
I-Hsuan Lin
▴ 10
4
votes
7
replies
1.9k
views
weird volcano plot
DESeq2
updated 21 months ago by
Shuning
• 0 • written 2.1 years ago by
shouzheng
▴ 10
0
votes
1
reply
751
views
DEseq2 dispersion plot
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Emma
• 0
1
vote
0
replies
706
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc2024
22 months ago • updated 21 months ago
shepherl
4.2k
0
votes
2
replies
1.1k
views
News:
BioC2024 abstract submission is open!
BioC2024
Conference
Bioconductor
written 22 months ago by
Maria Doyle
▴ 110
0
votes
0
replies
624
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
21 months ago
Giovanni Calice
▴ 160
0
votes
0
replies
1.1k
views
Job:
Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics
JobPosting
SingleCell
Spatial
SpatialExperiment
21 months ago
Peter Hickey
▴ 760
1
vote
3
replies
2.2k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
21 months ago • updated 15 months ago
s.malik
• 0
0
votes
0
replies
1.0k
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Andrew
• 0
0
votes
0
replies
690
views
News:
Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
21 months ago
info
▴ 10
1
vote
1
reply
1.2k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 21 months ago by
Wei Shi
★ 3.6k • written 22 months ago by
Alex
• 0
0
votes
1
reply
571
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Fabian
• 0
1
vote
3
replies
1.1k
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 21 months ago by
swbarnes2
★ 1.4k • written 21 months ago by
sap275
▴ 10
0
votes
11
replies
1.9k
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 21 months ago by
Gordon Smyth
53k • written 22 months ago by
mico
• 0
0
votes
2
replies
1.1k
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Suvi
• 0
8
votes
6
replies
1.3k
views
DGE analysis with LIMMA
limma
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Amit
• 0
0
votes
0
replies
789
views
News:
BioC2024 registration is now open!
BioC2024
Conference
Bioconductor
Community
21 months ago
Maria Doyle
▴ 110
0
votes
1
reply
897
views
error in Matrix function
MatrixQCvis
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Bharti
• 0
0
votes
3
replies
959
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
MEME
▴ 10
1
vote
0
replies
773
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
21 months ago
jk
▴ 10
0
votes
0
replies
596
views
Can I combine collinear variables into a single value
BatchEffect
limma
21 months ago
Harrsha
• 0
0
votes
1
reply
709
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2
pheatmap
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
zhangaimei
• 0
6
votes
5
replies
2.3k
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 21 months ago by
Kim
• 0
1
vote
4
replies
1.0k
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
21 months ago
hmillike
• 0
0
votes
0
replies
1.1k
views
Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please…
ASpli
21 months ago
vipul14
• 0
0
votes
0
replies
639
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
21 months ago
danalvoronov
▴ 10
2
votes
1
reply
1.2k
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon
clusterPro
Salmosalar
AnnotationHub
GeneOntology
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Filipe
• 0
0
votes
1
reply
720
views
ExactTest vs QLFTest
edgeR
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
fr8712ca-s
• 0
0
votes
2
replies
777
views
arm64 Update to flowWorkspace (4.14.2)
flowWorkspace
21 months ago
rgong1
• 0
0
votes
0
replies
519
views
lfcSE
RGSEA
21 months ago
Gordon
• 0
0
votes
1
reply
685
views
Matrix multiplication error to estimate telomere length
methylclockData
minfi
methylclock
minfidata
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
sharangiiv
• 0
0
votes
3
replies
926
views
impute.knn produces different results based on matrix order
impute
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Tamara
• 0
0
votes
1
reply
486
views
few significant genes from DESeq2 analysis
DESeq2
updated 21 months ago by
Michael Love
43k • written 21 months ago by
Ming
• 0
0
votes
3
replies
1.2k
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Laura
• 0
1
vote
2
replies
1.8k
views
Impute does not work
impute
22 months ago • updated 21 months ago
Laura
• 0
2
votes
3
replies
1.1k
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
21 months ago
jbgnielson
• 0
0
votes
4
replies
1.1k
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
21 months ago
mperalc
• 0
0
votes
2
replies
1.2k
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
ryann
• 0
1
vote
7
replies
1.8k
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
updated 14 months ago by
juansmurphy
• 0 • written 22 months ago by
mico
• 0
0
votes
0
replies
628
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
22 months ago
thomas.heigl.ibk
• 0
0
votes
1
reply
1.9k
views
error in mapIds function
mapIds
biomaRt
updated 22 months ago by
Marcel Ramos
700 • written 22 months ago by
Regina
• 0
1
vote
4
replies
1.5k
views
DEseq2 coefficient
DESeq2
coefficient
22 months ago • updated 19 months ago
JKim
• 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 21 months ago by
Michael Love
43k • written 22 months ago by
sap275
▴ 10
2
votes
1
reply
760
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 22 months ago by
Michael Love
43k • written 22 months ago by
sap275
▴ 10
0
votes
1
reply
768
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 22 months ago by
ATpoint
★ 5.0k • written 22 months ago by
sodiogoes
• 0
2
votes
2
replies
846
views
locfunc not found in DESeq2
locfunc
DESeq2
shorth
estimateSizeFactors
22 months ago
Hope
▴ 10
46,696 results • Page
30 of 934
Recent ...
Replies
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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