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biobase
•
reset
3
votes
3
replies
248
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
1
vote
4
replies
622
views
Help for SeqVarData function
Biobase
SeqVarTools
9 months ago
pjuge
• 0
2
votes
4
replies
1.4k
views
Failed to install Biobase
GSVA
Biobase
updated 13 months ago by
James W. MacDonald
66k • written 14 months ago by
johann.brisseau
• 0
0
votes
2
replies
1.0k
views
Automatically disconnecting database connections stored within an S4 object
DBI
S4
Biobase
updated 21 months ago by
Hervé Pagès
16k • written 21 months ago by
sandmann.t
▴ 70
0
votes
1
reply
3.0k
views
NMF installation with current R version
NMF
Biobase
updated 24 months ago by
shepherl
3.9k • written 2.0 years ago by
Abhishek
• 0
2
votes
1
reply
1.7k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 2.3 years ago by
James W. MacDonald
66k • written 2.3 years ago by
NGS_enthusiast
• 0
2
votes
3
replies
2.0k
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages
Biobase
updated 2.5 years ago by
ATpoint
★ 4.1k • written 2.5 years ago by
Elizabeth Purdom
▴ 210
2
votes
0
replies
634
views
PREDA shiny Golem issue
PREDAsampledata
PREDA
Biobase
2.5 years ago
Gavin
▴ 20
0
votes
2
replies
990
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
2.7 years ago
sogol.bouyeh
• 0
3
votes
4
replies
2.1k
views
R session aborted: prcomp
Biobase
stats
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
Gero
• 0
0
votes
0
replies
868
views
Job:
Cancer Bioinformatician @ University of East Anglia - Norwich Medical School, UK
cancer
postdoc
biomarkers
Biobase
3.2 years ago
Daniel Brewer
▴ 100
0
votes
0
replies
922
views
Job:
Senior Research Associate in Bioinformatics @ University of East Anglia - Norwich Medical School, UK
Biobase
bioinformatics
biomarkers
cancer
3.4 years ago
Daniel Brewer
▴ 100
0
votes
3
replies
1.4k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools
ReadAffy
Biobase
phenoData
affy
updated 3.4 years ago by
James W. MacDonald
66k • written 3.4 years ago by
bastien_chassagnol
• 0
0
votes
0
replies
704
views
Job:
Postdoctoral Associate position to study hematopoietic neoplasms using advanced single-cell multi-omics technologies
Biobase
3.4 years ago
NamLab
• 0
0
votes
0
replies
694
views
Job:
Data analyst position to study hematopoietic neoplasms via single-cell multi-omics
Biobase
3.4 years ago
NamLab
• 0
0
votes
1
reply
699
views
Calculations (averaging and normalization) with expressionset
RTCA
Biobase
Bioconductor
expressionset
updated 3.5 years ago by
James W. MacDonald
66k • written 3.5 years ago by
VanessaOak
• 0
1
vote
0
replies
807
views
Job:
Computational Biologist at Denali Therapeutics
Biobase
biomarker
neuroscience
biotech
3.5 years ago
sandmann.t
▴ 70
1
vote
3
replies
907
views
After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI
Biobase
3.6 years ago
Axel Klenk
★ 1.0k
4
votes
8
replies
2.3k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma
biobase
ExpressionSet
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
sa825
• 0
0
votes
0
replies
888
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error
biobase
Iranges
ArrayExpressHTS
4.2 years ago
Ed Siefker
▴ 230
0
votes
3
replies
1.7k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo
biobase
GEOquery
updated 4.6 years ago by
James W. MacDonald
66k • written 4.6 years ago by
salamandra
▴ 20
3
votes
3
replies
1.9k
views
Is there a way to save and open an expression set?
biobase
updated 4.6 years ago by
Kevin Blighe
★ 3.9k • written 4.6 years ago by
salamandra
▴ 20
0
votes
5
replies
2.1k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 4.9 years ago by
James W. MacDonald
66k • written 4.9 years ago by
Seymoo
• 0
2
votes
4
replies
2.5k
views
error: namespace Loading DESeq2
deseq2
error namespace
biobase
updated 5.4 years ago by
James W. MacDonald
66k • written 5.4 years ago by
jpcourneya
• 0
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
5.5 years ago
cschot3
• 0
4
votes
8
replies
2.4k
views
ALL dataset, correct syntax using the exprs call?
ALL
bioconductor
biobase
exprs
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
detroit.drive
• 0
2
votes
2
replies
1.2k
views
aaMap Import "Not Available"
bioconductor
biobase
aaMap
updated 5.8 years ago by
rreck
▴ 20 • written 5.8 years ago by
detroit.drive
• 0
5
votes
7
replies
1.5k
views
Difficulty extending ExpressionSet
biobase
expressionset
eset
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
andrew.birnberg
▴ 20
2
votes
2
replies
4.5k
views
AnnotatedDataFrame is not a defined class
annotatedDataFrame
R
Biobase
9.5 years ago • updated 5.8 years ago
nonCodingGene
▴ 10
2
votes
10
replies
1.8k
views
Am I on the right tracks with a 3 factor design in Limma?
r
limma
design matrix
biobase
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
reubenmcgregor88
• 0
2
votes
2
replies
2.4k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray
biobase
5.9 years ago
charlesgwellem
▴ 10
8
votes
2
replies
3.0k
views
exprs function - clash with dplyr
exprs
dplyr
Biobase
6.0 years ago
Wolfgang Huber
★ 13k
1
vote
3
replies
1.5k
views
Boxplot and Identification of DEG
limma
biobase
geoquery
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
nia
▴ 30
2
votes
3
replies
1.7k
views
GEOquery problem in calling the function in Rstudio
R
software error
biobase
geoquery
updated 6.8 years ago by
James W. MacDonald
66k • written 6.8 years ago by
jemaatita
• 0
4
votes
3
replies
1.2k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays
expressionset
biobase
annotation
brainarray
updated 6.9 years ago by
James W. MacDonald
66k • written 6.9 years ago by
lykhenko.olexandr
• 0
0
votes
1
reply
1.1k
views
Problem Subsetting ExpressionSet
expressionset
biobase
bioconductor
updated 7.0 years ago by
James W. MacDonald
66k • written 7.0 years ago by
Tom Oates
▴ 60
1
vote
2
replies
3.1k
views
how to update feature data with different dimensions in expressionSet?
biobase
eSet
expressionSet
updated 7.6 years ago by
Martin Morgan
25k • written 7.6 years ago by
Guido Hooiveld
★ 4.0k
6
votes
13
replies
2.0k
views
Comparison of Column of AnnotatedDataFrame
biobase
AnnotatedDataFrame
7.6 years ago
Dario Strbenac
★ 1.5k
0
votes
4
replies
1.3k
views
`exprs<-` Allows setting assay data matrix size that doesn't match se.exprs
Biobase
updated 7.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.8 years ago by
psmirnov2000
• 0
1
vote
2
replies
2.5k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase
convert
sva
ringo
arrayqualitymetrics
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
chris.rock
• 0
2
votes
2
replies
8.0k
views
Convert Expression Set into a Matrix or Data Frame
microarray
biobase
affy
R
updated 8.3 years ago by
Diego Diez
▴ 760 • written 8.3 years ago by
hshabbeer.09
• 0
0
votes
2
replies
1.4k
views
Help with annotating eset (Affy Arrays)
Biobase
annotationdbi
affy
microarray
8.5 years ago
rumroses12
• 0
2
votes
5
replies
3.8k
views
How to use t.test to select best features out of multiple features?
microarray
biobase
feature selection
t.test
R
updated 8.7 years ago by
svlachavas
▴ 830 • written 8.7 years ago by
babumanish837
▴ 10
1
vote
3
replies
3.1k
views
How to use expression set object to select genes using different gene selection methods
microarray
biobase
geoquery
updated 8.7 years ago by
svlachavas
▴ 830 • written 8.7 years ago by
babumanish837
▴ 10
0
votes
1
reply
3.1k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray
biobase
expresiondataset
r
8.7 years ago
floodking
• 0
0
votes
1
reply
5.8k
views
pvca error (Error in Data$variables : $ operator is invalid for atomic vectors)
pvca
biobase
updated 8.8 years ago by
erflynn
• 0 • written 9.1 years ago by
a.riedel
• 0
4
votes
6
replies
5.2k
views
Proper way to build phenoData object?
limma
affy
biobase
updated 9.3 years ago by
Guido Hooiveld
★ 4.0k • written 9.3 years ago by
chandlerjd58
▴ 10
1
vote
3
replies
2.4k
views
Error installing Biobase on R 3.1.2
biobase
updated 9.3 years ago by
Johannes Rainer
★ 2.0k • written 9.3 years ago by
yannick.lippi
• 0
0
votes
2
replies
1.3k
views
How to Represent Data from Various Different Assays in a Single Class?
biobase
updated 9.4 years ago by
Levi Waldron
★ 1.1k • written 9.4 years ago by
cannin
▴ 20
0
votes
3
replies
1.6k
views
conflict in names between phenoData and protocolData during RMA
biobase
9.5 years ago
bin.shan
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq?
by
baptiste.bidon
• 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
66k
Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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★ 6.5k
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▴ 10
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Gordon Smyth
50k
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landenshanie
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