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plotMA difference using or not a sub matrix
matrixsubset
plotMA
just now
l.troxler
• 0
0
votes
1
reply
66
views
DepMap copy number
software error
depmap
updated 51 minutes ago by
Laurent Gatto
1.5k • written 6 months ago by
DannyM
• 0
0
votes
1
reply
17
views
High fold change reported for comparison of samples with zero values in all samples
edgeR
updated 1 hour ago by
James W. MacDonald
56k • written 4 hours ago by
Laura
• 0
0
votes
1
reply
16
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 1 hour ago by
Mike Smith
★ 4.9k • written 4 hours ago by
Jeremy
• 0
0
votes
1
reply
12
views
Warning in EnhancedVolcano plot
volcano-plot
EnhancedVolcano
updated 4 hours ago by
Kevin Blighe
2.7k • written 4 hours ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
44
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Sample quality weights for RNA-seq
DESeq2
limma
weight
14 hours ago • updated 1 hour ago
Naomi Altman
★ 6.0k
0
votes
1
reply
21
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DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 5 hours ago by
Kevin Blighe
2.7k • written 8 hours ago by
dorina.jamniczky
• 0
0
votes
3
replies
24
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Error following instructions of CBioportal R-workshop example 2
MultiAssayExperiment
cBioPortalData
updated 4 hours ago by
Kevin Blighe
2.7k • written 7 hours ago by
Javier
• 0
0
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0
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10
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Warning with the example of GSEA
fgsea
fgse
6 hours ago
julie.hardy
• 0
0
votes
0
replies
11
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discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
7 hours ago
xiaofeiwang18266
▴ 20
0
votes
0
replies
8
views
layout has more positions than samples but omixerRand doesn't randomize the samples
Omixer
8 hours ago
Lluís Revilla Sancho
▴ 630
0
votes
0
replies
14
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
13 hours ago
ikumar2000
• 0
0
votes
1
reply
42
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
updated 13 hours ago by
Michael Love
32k • written 1 day ago by
demisa
• 0
0
votes
1
reply
21
views
EnhancedVolcano plot with colCustom
EnhancedVolcano
updated 16 hours ago by
Kevin Blighe
2.7k • written 16 hours ago by
neeraja149vegesna
• 0
0
votes
2
replies
43
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
21 hours ago • updated 17 hours ago
Kate
• 0
1
vote
1
reply
34
views
Enhanced Volcano Plot Controlling Color Layers
EnhancedVolcano
1 day ago • updated 23 hours ago
dk0319
• 0
4
votes
2
replies
49
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 1 day ago by
James W. MacDonald
56k • written 1 day ago by
Gero
• 0
0
votes
0
replies
15
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Missing sample
OSAT
1 day ago
Lluís Revilla Sancho
▴ 630
0
votes
1
reply
39
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Query regarding edgeR and limma
limma
readDGE
edgeR
updated 1 day ago by
James W. MacDonald
56k • written 2 days ago by
abhisekdey061
• 0
0
votes
0
replies
18
views
News:
Terra / AnVIL R / Bioconductor Popup Workshops
AnVIL
workshop
Bioconductor
Terra
1 day ago
shepherl
2.6k
0
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0
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14
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News:
Bioconductor Release 3.12 and Bioconductor Devel 3.13 Code Freeze Deadlines!
deadline
Bioconductor
devel
release
1 day ago
shepherl
2.6k
0
votes
0
replies
19
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Duplicate row.names when building SummarizedExperiment with make_se in DEP
DEP
1 day ago
hele7
▴ 20
0
votes
0
replies
17
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Job:
Biostatistics Research Associate, York, UK
QTL
fourier
TimeSeriesExperiment
timecoursedata
1 day ago
Daphne
• 0
0
votes
0
replies
28
views
How can I correctly normalize RNA--seq data and find DEGs in complicated data set with ImpluseDE2?
ImpluseDE2
1 day ago • updated 15 hours ago
MU
• 0
1
vote
1
reply
42
views
simplifyEnrichment install error
package
Rversion
Install
simplifyEnrichment
updated 1 day ago by
shepherl
2.6k • written 1 day ago by
ch_el
▴ 10
3
votes
9
replies
256
views
Couldn't load org.Hs.eg.db
org.Hs.eg.db
updated 2 hours ago by
Xulei Huo
• 0 • written 1 day ago by
Chen
▴ 10
3
votes
3
replies
61
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 1 day ago by
Michael Love
32k • written 2 days ago by
Tom
• 0
0
votes
8
replies
113
views
Problem with estimateSizeFactors due to avgTxLength
DESeq2
updated 13 hours ago by
Michael Love
32k • written 1 day ago by
Mark
• 0
32
votes
23
replies
1.2k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 2 hours ago by
Xulei Huo
• 0 • written 3 days ago by
Arun
▴ 140
0
votes
0
replies
28
views
News:
Nominations for Bioconductor 2021 Awards!
Awards
Recognition
Bioconductor
Bioc2021
2 days ago
shepherl
2.6k
0
votes
0
replies
23
views
News:
Bioconductor 3.13 New Package Submission Deadline
release
Submission
newpackage
Release
Deadline
2 days ago
shepherl
2.6k
0
votes
0
replies
24
views
News:
Bioconductor Release 3.13 Schedule
Release
release
2 days ago
shepherl
2.6k
1
vote
1
reply
39
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 2 days ago by
Michael Love
32k • written 2 days ago by
xiaofeiwang18266
▴ 20
0
votes
2
replies
47
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta
BiocFileCache
updated 2 days ago by
Michael Love
32k • written 2 days ago by
judith.risse
• 0
0
votes
0
replies
37
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl
minfi
2 days ago
jefflincoln4
• 0
4
votes
4
replies
81
views
DESeq2 two conditions with interaction
DESeq2
updated 1 day ago by
swbarnes2
▴ 680 • written 2 days ago by
mboeck
• 0
0
votes
2
replies
238
views
News:
List of Deprecated Packages for Bioc3.13
Workflow
Software
Deprecation
ExperimentData
4 months ago • updated 2 days ago
shepherl
2.6k
0
votes
4
replies
77
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma
edgeR
rna
3 days ago • updated 2 days ago
Nirad
• 0
0
votes
0
replies
27
views
News:
Bioc2021 Registration is Open
Conference
Bioc2021
2 days ago
shepherl
2.6k
0
votes
0
replies
20
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3 days ago • updated 2 days ago
Sam
▴ 10
0
votes
1
reply
55
views
DEseq2 to test half-life for time-series data
half-life
DESeq2
time-series
updated 3 days ago by
Michael Love
32k • written 5 days ago by
Xianjun Dong
• 0
0
votes
4
replies
98
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
5 days ago • updated 18 hours ago
jbono
• 0
4
votes
5
replies
100
views
edgeR for a mixture experiment
edgeR
model-selection
RRBS
mixture-experiment
3 days ago
ingerslev
• 0
1
vote
2
replies
73
views
BiomaRt conversion
biomaRt
27 days ago • updated 3 days ago
gwendal.lazennec
• 0
0
votes
0
replies
28
views
how to construct a SNPlocs-class by myself
BSgenome
SNPlocs
3 days ago
shangguandong1996
▴ 20
0
votes
2
replies
71
views
CRISPRseek package: 5’ PAM?
CRISPRseek
6 days ago • updated 3 days ago
nderian
• 0
3
votes
2
replies
65
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData
ArrayExpress
updated 3 days ago by
Gordon Smyth
42k • written 4 days ago by
Gero
• 0
0
votes
1
reply
53
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 3 days ago by
Guido Hooiveld
★ 2.9k • written 4 days ago by
Pierre-Alex
• 0
4
votes
4
replies
82
views
How to save multiple assays and subsequent processed data in single SummarizedExperiment Object
SummarizedExperiment
updated 3 days ago by
Laurent Gatto
1.5k • written 4 days ago by
rohitsatyam102
▴ 10
0
votes
0
replies
228
views
Job:
Bioinformatics Laboratory Head, WEHI, Melbourne, Australia
Australia
JobPosting
4 days ago
Gordon Smyth
42k
40,558 results • Page
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Answer: DepMap copy number
by
Laurent Gatto
1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp
by
James W. MacDonald
56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq
by
Naomi Altman
★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile
by
Mike Smith
★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db
by
Xulei Huo
• 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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