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biobase
•
reset
3
votes
3
replies
138
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
7 days ago • updated 1 day ago
jacques.imbert
• 0
1
vote
4
replies
551
views
Help for SeqVarData function
Biobase
SeqVarTools
8 months ago
pjuge
• 0
2
votes
4
replies
1.3k
views
Failed to install Biobase
GSVA
Biobase
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
johann.brisseau
• 0
0
votes
2
replies
983
views
Automatically disconnecting database connections stored within an S4 object
DBI
S4
Biobase
updated 20 months ago by
Hervé Pagès
16k • written 20 months ago by
sandmann.t
▴ 70
0
votes
1
reply
2.8k
views
NMF installation with current R version
NMF
Biobase
updated 23 months ago by
shepherl
3.8k • written 23 months ago by
Abhishek
• 0
2
votes
1
reply
1.6k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
NGS_enthusiast
• 0
2
votes
3
replies
1.9k
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages
Biobase
updated 2.4 years ago by
ATpoint
★ 4.0k • written 2.4 years ago by
Elizabeth Purdom
▴ 210
2
votes
0
replies
610
views
PREDA shiny Golem issue
PREDAsampledata
PREDA
Biobase
2.4 years ago
Gavin
▴ 20
0
votes
2
replies
933
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
2.6 years ago
sogol.bouyeh
• 0
3
votes
4
replies
2.0k
views
R session aborted: prcomp
Biobase
stats
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
Gero
• 0
0
votes
0
replies
836
views
Job:
Cancer Bioinformatician @ University of East Anglia - Norwich Medical School, UK
cancer
postdoc
biomarkers
Biobase
3.1 years ago
Daniel Brewer
▴ 100
0
votes
0
replies
891
views
Job:
Senior Research Associate in Bioinformatics @ University of East Anglia - Norwich Medical School, UK
Biobase
bioinformatics
biomarkers
cancer
3.3 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 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
bastien_chassagnol
• 0
0
votes
0
replies
681
views
Job:
Postdoctoral Associate position to study hematopoietic neoplasms using advanced single-cell multi-omics technologies
Biobase
3.3 years ago
NamLab
• 0
0
votes
0
replies
675
views
Job:
Data analyst position to study hematopoietic neoplasms via single-cell multi-omics
Biobase
3.3 years ago
NamLab
• 0
0
votes
1
reply
676
views
Calculations (averaging and normalization) with expressionset
RTCA
Biobase
Bioconductor
expressionset
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
VanessaOak
• 0
1
vote
0
replies
785
views
Job:
Computational Biologist at Denali Therapeutics
Biobase
biomarker
neuroscience
biotech
3.4 years ago
sandmann.t
▴ 70
1
vote
3
replies
878
views
After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI
Biobase
3.5 years ago
Axel Klenk
★ 1.0k
4
votes
8
replies
2.2k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma
biobase
ExpressionSet
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
sa825
• 0
0
votes
0
replies
868
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error
biobase
Iranges
ArrayExpressHTS
4.1 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 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
salamandra
▴ 20
3
votes
3
replies
1.8k
views
Is there a way to save and open an expression set?
biobase
updated 4.5 years ago by
Kevin Blighe
★ 3.9k • written 4.5 years ago by
salamandra
▴ 20
0
votes
5
replies
2.0k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 4.8 years ago by
James W. MacDonald
65k • written 4.8 years ago by
Seymoo
• 0
2
votes
4
replies
2.4k
views
error: namespace Loading DESeq2
deseq2
error namespace
biobase
updated 5.3 years ago by
James W. MacDonald
65k • written 5.3 years ago by
jpcourneya
• 0
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
5.4 years ago
cschot3
• 0
4
votes
8
replies
2.3k
views
ALL dataset, correct syntax using the exprs call?
ALL
bioconductor
biobase
exprs
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
detroit.drive
• 0
2
votes
2
replies
1.2k
views
aaMap Import "Not Available"
bioconductor
biobase
aaMap
updated 5.7 years ago by
rreck
▴ 20 • written 5.7 years ago by
detroit.drive
• 0
5
votes
7
replies
1.5k
views
Difficulty extending ExpressionSet
biobase
expressionset
eset
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
andrew.birnberg
▴ 20
2
votes
2
replies
4.4k
views
AnnotatedDataFrame is not a defined class
annotatedDataFrame
R
Biobase
9.4 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 5.8 years ago by
Gordon Smyth
50k • written 5.8 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
5.8 years ago
charlesgwellem
▴ 10
8
votes
2
replies
3.0k
views
exprs function - clash with dplyr
exprs
dplyr
Biobase
5.9 years ago
Wolfgang Huber
★ 13k
1
vote
3
replies
1.5k
views
Boxplot and Identification of DEG
limma
biobase
geoquery
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 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
65k • 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 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
lykhenko.olexandr
• 0
0
votes
1
reply
1.1k
views
Problem Subsetting ExpressionSet
expressionset
biobase
bioconductor
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
Tom Oates
▴ 60
1
vote
2
replies
3.0k
views
how to update feature data with different dimensions in expressionSet?
biobase
eSet
expressionSet
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
Guido Hooiveld
★ 3.9k
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 7.7 years ago by
psmirnov2000
• 0
1
vote
2
replies
2.4k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase
convert
sva
ringo
arrayqualitymetrics
updated 8.1 years ago by
Gordon Smyth
50k • written 8.1 years ago by
chris.rock
• 0
2
votes
2
replies
7.9k
views
Convert Expression Set into a Matrix or Data Frame
microarray
biobase
affy
R
updated 8.2 years ago by
Diego Diez
▴ 760 • written 8.2 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 8.6 years ago by
svlachavas
▴ 830 • written 8.6 years ago by
babumanish837
▴ 10
1
vote
3
replies
3.0k
views
How to use expression set object to select genes using different gene selection methods
microarray
biobase
geoquery
updated 8.6 years ago by
svlachavas
▴ 830 • written 8.6 years ago by
babumanish837
▴ 10
0
votes
1
reply
3.0k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray
biobase
expresiondataset
r
8.6 years ago
floodking
• 0
0
votes
1
reply
5.7k
views
pvca error (Error in Data$variables : $ operator is invalid for atomic vectors)
pvca
biobase
updated 8.7 years ago by
erflynn
• 0 • written 9.0 years ago by
a.riedel
• 0
4
votes
6
replies
5.2k
views
Proper way to build phenoData object?
limma
affy
biobase
updated 9.2 years ago by
Guido Hooiveld
★ 3.9k • written 9.2 years ago by
chandlerjd58
▴ 10
1
vote
3
replies
2.4k
views
Error installing Biobase on R 3.1.2
biobase
updated 9.2 years ago by
Johannes Rainer
★ 2.0k • written 9.2 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 9.3 years ago by
Levi Waldron
★ 1.1k • written 9.3 years ago by
cannin
▴ 20
0
votes
3
replies
1.5k
views
conflict in names between phenoData and protocolData during RMA
biobase
9.5 years ago
bin.shan
• 0
50 results • Page
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Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) …
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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