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Votes
32
votes
0
replies
38k
views
limma moderated t-statistics and B-statistics
Microarray
limma
19.5 years ago • updated 3.4 years ago
Gordon Smyth
50k
0
votes
0
replies
33k
views
Why the resuts are so different between the classic and the glm methods?
edgeR
edgeR
10.3 years ago
Jiantao Yu
▴ 10
3
votes
8
replies
25k
views
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
BiocUpgrade
Rstudio
Bioconductor
R3.2.2
8.4 years ago
svlachavas
▴ 830
0
votes
0
replies
17k
views
1000 R tutorials/Links
Sequencing
Microarray
Genetics
Visualization
Network
Bayesian
Classification
Clustering
13.8 years ago
David Lyon
▴ 340
2
votes
13
replies
14k
views
Issues connecting with R 3.2.2 to source("http://bioconductor.org/biocLite.R")
spade
8.4 years ago
frostbite907
• 0
33
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.5 years ago • updated 18 months ago
Michael Love
41k
0
votes
0
replies
12k
views
Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors
Cancer
convert
Cancer
convert
12.4 years ago
Chao-Jen Wong
▴ 580
0
votes
6
replies
11k
views
Package version of Bioconductor cannot be unloaded, Error in unloadNamespace(package),help!!
microarray
software error
hgu133plus2.db
updated 4.9 years ago by
Martin Morgan
25k • written 4.9 years ago by
naf
• 0
1
vote
1
reply
11k
views
Pheatmap clustering and row annotation
R
pheatmap
cutree
6.5 years ago
meseretbrihanu
▴ 10
1
vote
4
replies
10k
views
Couldn't install GenomicRanges packages after update bioconductor to 3.2 version ?
bioconductor
error handling
8.2 years ago
Jurat Shahidin
▴ 80
1
vote
3
replies
9.5k
views
Sorting columns in pheatmap
pheatmap
updated 2.9 years ago by
Chris Seidel
▴ 80 • written 2.9 years ago by
Linda
• 0
0
votes
0
replies
8.8k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray
Annotation
Preprocessing
hgu133plus2
hgug4112a
virtualArray
Microarray
hgug4112a
9.8 years ago
Guest User
★ 13k
0
votes
2
replies
8.6k
views
Clusterprofiler error: No gene can be mapped
software error
go
annotation
clusterProfiler
updated 11 months ago by
tarltonuk2089
• 0 • written 4.0 years ago by
tianshenbio
• 0
2
votes
3
replies
8.2k
views
Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common.]
GreyListChIP
6.4 years ago
kyliecode
• 0
4
votes
9
replies
7.7k
views
Upper triangular matrix heatmap using pheatmap package
pheatmap
8.3 years ago
Deepak Tanwar
▴ 10
2
votes
9
replies
7.4k
views
Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
deseq
deseq2
edger
tophat
bowtie
8.8 years ago
ysdel
▴ 40
8
votes
4
replies
6.9k
views
Can't upgrade to Bioconductor 3.3?
bioconductor
biocupgrade
upgrade
update
bioclite
7.9 years ago
enricoferrero
▴ 660
2
votes
11
replies
6.8k
views
ClusterProfiler enrichGO function leads to different enrichment results in different computers, while the code and gene list keep same
clusterProfiler
2.3 years ago
liuzhy
▴ 10
6
votes
6
replies
6.7k
views
Avoid upgrading BiocManager to 1.30.13; fix proposed
BiocManager
updated 2.6 years ago by
Mengfei
• 0 • written 2.9 years ago by
Vincent J. Carey, Jr.
6.7k
0
votes
6
replies
6.6k
views
Bioconductor 3.0 and old versions with R 3.2.0
package updates
8.8 years ago
Cataphractus
• 0
4
votes
4
replies
6.4k
views
what the test method for enrichGO in clusterProfiler?
clusterProfiler
2.3 years ago
xiaofeiwang18266
▴ 50
0
votes
0
replies
6.4k
views
Pheatmap: how to use breaks for pheatmap
pheatmap
heatmap
7.4 years ago
jarod_v6@libero.it
▴ 40
0
votes
0
replies
6.3k
views
maSigPro error PlotGroups [Error: (list) object cannot be coerced to type 'double']
masigpro
error
PlotGroups
6.8 years ago
nicolas.descostes
▴ 20
0
votes
2
replies
6.1k
views
Unable to install any bioconductor packages
R
biocinstaller
bioclite
package installation
6.6 years ago
sebastien200109
• 0
4
votes
15
replies
6.1k
views
mzR installation error: "unable to load shared object"
mzR
installation
8.7 years ago
Eugene
• 0
2
votes
6
replies
6.0k
views
color scale in cnetplot (enrichplot) is not centered in 0, skewed towards positive values
enrichplot
clusterProfiler
3.3 years ago • updated 3.2 years ago
Emilia
▴ 30
2
votes
10
replies
6.0k
views
Install older specific version from an R package that is on the Bioconductor Repository
Bioconductor
biocLite
R packages
oldversion
8.4 years ago
svlachavas
▴ 830
2
votes
11
replies
5.9k
views
biomaRT connexion problem make failed my unit tests
biomaRt
Peer's Certificate
Ensembl
updated 3.2 years ago by
Mike Smith
★ 6.5k • written 3.5 years ago by
ilysR
• 0
0
votes
18
replies
5.7k
views
WGCNA error in network construction ?
microarray
rnaseq
7.0 years ago
m.azhar
▴ 10
0
votes
2
replies
5.5k
views
What does this mean?
software error
8.1 years ago
xlyan011
• 0
2
votes
11
replies
5.3k
views
Error: cannot allocate vector of size ...MB
limma
8.2 years ago
fahime.falahi
• 0
1
vote
3
replies
5.2k
views
Not able to install packages in Bioconductor version '3.16'
Install
BiocManager
version3.16
updated 14 months ago by
shepherl
3.8k • written 16 months ago by
Tonmoya
• 0
0
votes
0
replies
5.1k
views
a question about input agilent single-channel data to R ( using limma package). Thanks for your kind help.
affy
affy
12.5 years ago
liuyang zhao
▴ 20
0
votes
0
replies
5.0k
views
Reading GFF files into R and GenomeGraphs
Coverage
Annotation
Visualization
convert
GLAD
GenomeGraphs
rtracklayer
IRanges
Coverage
14.6 years ago
Michael Dondrup
▴ 140
1
vote
21
replies
5.0k
views
Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0
BiocManager
written 3.9 years ago by
Lucy
▴ 60
0
votes
3
replies
4.9k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges
genomicra
updated 2.4 years ago by
James W. MacDonald
65k • written 2.4 years ago by
Alexandre
• 0
0
votes
3
replies
4.8k
views
ridgeplot doesn't work: Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero
clusterProfiler
updated 17 months ago by
mttrantrietminh
• 0 • written 20 months ago by
Y.K
• 0
2
votes
8
replies
4.7k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 20 months ago by
1526466763
• 0 • written 24 months ago by
e.iich
• 0
1
vote
2
replies
4.7k
views
rhdf5 package fails to install
rhdf5
hdf5
8.5 years ago
trombe.piju
• 0
4
votes
4
replies
4.7k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.4 years ago
k___
▴ 30
1
vote
3
replies
4.6k
views
Load FlowCore to read .fcs files in R
flowcore
flow cytometry
R
5.8 years ago
Bayram Sarilmaz
• 0
0
votes
1
reply
4.6k
views
Can't install package because of sp package
software error
8.4 years ago
MarcinKosiński
• 0
2
votes
3
replies
4.6k
views
WGCNA "bicor" correlation
wgcna
bicor
WGCNA
8.5 years ago
bcbio_uk
▴ 10
4
votes
6
replies
4.6k
views
How to design formula in DESeq2 when setting blind=FALSE in rlog transformation?
deseq2
normalization
9.4 years ago
Xianjun Dong
▴ 10
0
votes
1
reply
4.5k
views
Problems about installation
hguqiagenv3.db
updated 2.2 years ago by
shepherl
3.8k • written 2.2 years ago by
Jiafy3999
• 0
0
votes
6
replies
4.5k
views
Nonexistent include directory
software error
r package problem
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
kkp7700
• 0
0
votes
1
reply
4.5k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
4.6 years ago
444579004
• 0
2
votes
3
replies
4.4k
views
No gene set have size > 10 ...
clusterprofiler
gene ontology
5.4 years ago
anton.kratz
▴ 60
1
vote
12
replies
4.4k
views
WGCNA: correlations module-traits, and module membership-gene significance
WGCNA
co-expression analysis
gene significance
module membership
module-trait relationship
updated 21 months ago by
annamariabugaj
▴ 10 • written 4.5 years ago by
rodrigo.duarte88
▴ 30
0
votes
1
reply
4.4k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq
sample_table
phyloseq
9.2 years ago
Brian Smith
▴ 120
1,000 results • Page
1 of 20
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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