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Votes
3
votes
3
replies
3.1k
views
Problem installing rhdf5
rhdf5
6.6 years ago
jariani.abb
▴ 10
3
votes
0
replies
2.2k
views
DESeq2 with data containing 3 factors or more and outlier detection
10.0 years ago
Michael Love
41k
3
votes
6
replies
1.8k
views
Integer overflow issue with ChIPQC
ChIPQC
Rstudio
updated 4.8 years ago by
Martin Morgan
25k • written 4.8 years ago by
Nitesh Kumar Singh
▴ 30
3
votes
0
replies
3.7k
views
biocLite() fails to install all limma dependencies from CRAN
Cancer
limma
Cancer
limma
17.0 years ago
Seth Falcon
★ 7.4k
3
votes
0
replies
2.8k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray
Normalization
Bayesian
Regression
Cancer
limma
Microarray
Normalization
Cancer
13.0 years ago
Richard Friedman
★ 2.0k
3
votes
3
replies
2.5k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth
R
salmon rna seq
salmon
6.5 years ago
Walter F. Baumann
▴ 10
3
votes
2
replies
1.0k
views
ASpli readCounts never ends!
aspli
readCounts
rna-seq
alternative splicing
AS
5.2 years ago
fernandalpcosta
▴ 10
3
votes
9
replies
2.9k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles
AnnotationForge
Bimap
GO
9.6 years ago
artur
▴ 80
3
votes
0
replies
1.6k
views
What's the correct way to normalize HTseq files with TCGAbiolinks
normalization
R
rnaseq
bioconductor
6.6 years ago
eshelden
▴ 40
3
votes
5
replies
2.1k
views
Volcano plot - select additional gene
EnhancedVolcano
RNASeqR
R
volcanoplot
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
camillab.
▴ 10
3
votes
0
replies
704
views
DSS : Different results between DMLtest and DMLtest.multifactor
DSS
2.7 years ago
cer.chloe
▴ 30
3
votes
8
replies
1.3k
views
please someone help me to run this code
software error
R
8.3 years ago
Angel
▴ 40
3
votes
4
replies
2.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks
tcga
genomicdatacommon
5.7 years ago
franceschini.gianmarco
• 0
3
votes
6
replies
1.1k
views
How to replace NAs values in "CompressedIntegerList" objects [reproducible example is included] ?
r
bug
granges
8.1 years ago
Jurat Shahidin
▴ 80
3
votes
3
replies
1.4k
views
Retrieve accurate tumor stage data with TCGAbiolinks
tcgabiolinks
tcga
6.0 years ago
Benjamin Ostendorf
▴ 90
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.1 years ago • updated 2.0 years ago
Sarah_piggy
▴ 10
3
votes
3
replies
1.8k
views
Error running CellMix SampleAnalysis vignette
software error
cellmix
vignette
expressionset
7.3 years ago
gabor.halasz
• 0
3
votes
1
reply
429
views
NPARC package y-variable
NPARC
NPA
updated 7 months ago by
nils.kurzawa
▴ 20 • written 7 months ago by
Aidan
• 0
3
votes
9
replies
3.7k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.7 years ago
Gurkenkönig
▴ 10
3
votes
2
replies
1.2k
views
DEXSeq analysis with large number of samples
dexseq
estimatedispersions
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
nemanja.vucic
▴ 10
3
votes
0
replies
1.7k
views
Interpret topGO reults
topGO
reults
8.9 years ago
megerdes
▴ 40
3
votes
9
replies
2.3k
views
problem for finding soft thresholding in WGCNA algorithm
wgcna
abline function
Scale independence diagram
5.6 years ago
modarzi
▴ 10
3
votes
0
replies
1.7k
views
An appeal to flow cytometry tools users
flow
flowcore
flowworkspace
cytometry
gating
7.3 years ago
Greg Finak
▴ 240
3
votes
6
replies
1.6k
views
error using org.Hs.eg.db package : Error in get(load(file)) :
org.hs.eg.db
select
9.0 years ago
tina.khajeh
• 0
3
votes
5
replies
1.5k
views
Error in installing multiClust package
package installation
8.1 years ago
Shamim Sarhadi
▴ 20
3
votes
8
replies
26k
views
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
BiocUpgrade
Rstudio
Bioconductor
R3.2.2
8.5 years ago
svlachavas
▴ 830
3
votes
3
replies
950
views
IHW: retain annotation columns in data when running `ihw(pvalue ~ covariate, data = ...)`
ihw
independent hypothesis weighting
4.1 years ago
david.laehnemann
▴ 10
3
votes
4
replies
1.3k
views
Error in ChemmineR function propOB() and ChemmineOB prop_OB()
ChemmineR
ChemmineOB
updated 3.3 years ago by
Thomas Girke
★ 1.7k • written 3.4 years ago by
teresadijor
• 0
3
votes
1
reply
800
views
Export from limma, edit, import to same class
limma
8.8 years ago
jjotto
• 0
3
votes
4
replies
1.3k
views
Any way to detach or simplify nested GRangesList ?
grangeslist
filtering
r
7.6 years ago
Jurat Shahidin
▴ 80
3
votes
1
reply
914
views
ChIPQC 'Contigs of interest are not all in Bam file!!' error
ChIPQC
3.0 years ago
Jonah
▴ 20
3
votes
4
replies
1.8k
views
Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments
MultiAssayExperiment
curatedTCGAData
TCGAutils
3.4 years ago
svlachavas
▴ 830
3
votes
2
replies
946
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
2.1 years ago • updated 2.0 years ago
Dakarai
▴ 10
3
votes
2
replies
1.9k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq
fit
matrix
warning
updated 2.5 years ago by
koushik
• 0 • written 7.2 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
3
replies
647
views
RSS for new packages unavailable?
RSS
4.4 years ago
Malcolm Cook
★ 1.6k
3
votes
1
reply
2.4k
views
Problems installing Bioconductor -- pbkrtest
pbkrtest
8.4 years ago
codefused
▴ 30
3
votes
4
replies
1.5k
views
GEOquery:Get error sampleNames
geoquery
updated 5.3 years ago by
Bioconductor Community
0 • written 5.4 years ago by
ustcxyf
▴ 10
3
votes
4
replies
2.2k
views
STRINGdb: Error in download.file(urlStr, temp)
STRINGdb
R
updated 2.3 years ago by
damian.szk
▴ 80 • written 2.5 years ago by
qardessio
▴ 10
3
votes
4
replies
1.5k
views
Can't install packages on R or via Bioconductor
R
installation
packages
annotatr
biocmanager
4.1 years ago
dakarai_esgdaille
▴ 10
3
votes
5
replies
1.1k
views
why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor
Install
library
biocmanager
updated 9 months ago by
Vincent J. Carey, Jr.
6.7k • written 9 months ago by
Ndimensional
▴ 20
3
votes
4
replies
1.9k
views
Rhdf5lib Installation Problem - cp: cannot stat 'hdf5/c++/src/.libs/libhdf5_cpp.a'
software error
Rhdf5lib
5.0 years ago
z.navidi90
▴ 10
3
votes
0
replies
500
views
Creating qPCRset for nondetects anlaysis from QuantStudio data
nondetects
qPCR
qPCRData
3.0 years ago
jhackett
▴ 30
3
votes
2
replies
4.4k
views
Automatic color assignment for annotations on ComplexHeatmap
complexheatmap
6.7 years ago
CodeAway
▴ 70
3
votes
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
23 days ago
nhaus
▴ 30
3
votes
8
replies
2.6k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData
AnnotationForge
2.0 years ago
Saber_J
▴ 10
3
votes
3
replies
400
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 5 weeks ago by
alan.ocallaghan
▴ 160 • written 5 weeks ago by
Najla Abassi
• 0
3
votes
1
reply
1.8k
views
TwoSampleMR and ieugwasr
ieugwasr
clumping
TwoSampleMR
updated 7 weeks ago by
zoheir.alayash
▴ 10 • written 2.1 years ago by
S T
▴ 90
3
votes
5
replies
2.5k
views
ChIPQC - can't read in bam files
chipqc
chipqcreport
5.6 years ago
molly_the_minotaur
▴ 30
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
5.8 years ago
94133
• 0
3
votes
3
replies
3.3k
views
Modifying or writing a FCS file in R using the FlowCore package
FCS
flowframe
flowcore
flow cytometry
5.7 years ago
vonskopnik
▴ 10
1,000 results • Page
2 of 20
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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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…
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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