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biobase
•
reset
0
votes
4
replies
256
views
Newbie Question - adding metadata to an analysis
Biobase
23 days ago • updated 22 days ago
Bryan H
• 0
0
votes
0
replies
419
views
Job:
PhD-position in bioinformatics / computational biology
Epigenomics
NGS
Aging
Biobase
updated 7 months ago by
Michael Love
43k • written 7 months ago by
arne.sahm
• 0
3
votes
3
replies
819
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
9 months ago
jacques.imbert
• 0
1
vote
4
replies
930
views
Help for SeqVarData function
Biobase
SeqVarTools
17 months ago
pjuge
• 0
2
votes
4
replies
2.1k
views
Failed to install Biobase
GSVA
Biobase
updated 22 months ago by
James W. MacDonald
67k • written 22 months ago by
johann.brisseau
• 0
0
votes
2
replies
1.4k
views
Automatically disconnecting database connections stored within an S4 object
DBI
S4
Biobase
updated 2.4 years ago by
Hervé Pagès
16k • written 2.5 years ago by
sandmann.t
▴ 70
0
votes
1
reply
4.4k
views
NMF installation with current R version
NMF
Biobase
updated 2.7 years ago by
shepherl
4.1k • written 2.7 years ago by
Abhishek
• 0
2
votes
1
reply
2.1k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 3.0 years ago by
James W. MacDonald
67k • written 3.0 years ago by
NGS_enthusiast
• 0
2
votes
3
replies
3.0k
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages
Biobase
updated 3.2 years ago by
ATpoint
★ 4.6k • written 3.2 years ago by
Elizabeth Purdom
▴ 210
2
votes
0
replies
824
views
PREDA shiny Golem issue
PREDAsampledata
PREDA
Biobase
3.2 years ago
Gavin
▴ 20
0
votes
2
replies
1.3k
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
3.4 years ago
sogol.bouyeh
• 0
3
votes
4
replies
2.5k
views
R session aborted: prcomp
Biobase
stats
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
Gero
• 0
0
votes
0
replies
1.1k
views
Job:
Cancer Bioinformatician @ University of East Anglia - Norwich Medical School, UK
cancer
postdoc
biomarkers
Biobase
3.9 years ago
Daniel Brewer
▴ 100
0
votes
0
replies
1.1k
views
Job:
Senior Research Associate in Bioinformatics @ University of East Anglia - Norwich Medical School, UK
Biobase
bioinformatics
biomarkers
cancer
4.1 years ago
Daniel Brewer
▴ 100
0
votes
3
replies
1.7k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools
ReadAffy
Biobase
phenoData
affy
updated 4.1 years ago by
James W. MacDonald
67k • written 4.1 years ago by
bastien_chassagnol
• 0
0
votes
0
replies
876
views
Job:
Postdoctoral Associate position to study hematopoietic neoplasms using advanced single-cell multi-omics technologies
Biobase
4.1 years ago
NamLab
• 0
0
votes
0
replies
873
views
Job:
Data analyst position to study hematopoietic neoplasms via single-cell multi-omics
Biobase
4.1 years ago
NamLab
• 0
0
votes
1
reply
894
views
Calculations (averaging and normalization) with expressionset
RTCA
Biobase
Bioconductor
expressionset
updated 4.2 years ago by
James W. MacDonald
67k • written 4.2 years ago by
VanessaOak
• 0
1
vote
0
replies
976
views
Job:
Computational Biologist at Denali Therapeutics
Biobase
biomarker
neuroscience
biotech
4.2 years ago
sandmann.t
▴ 70
1
vote
3
replies
1.1k
views
After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI
Biobase
4.3 years ago
Axel Klenk
★ 1.0k
4
votes
8
replies
2.9k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma
biobase
ExpressionSet
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
sa825
• 0
0
votes
0
replies
1.1k
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error
biobase
Iranges
ArrayExpressHTS
4.9 years ago
Ed Siefker
▴ 230
0
votes
3
replies
2.0k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo
biobase
GEOquery
updated 5.3 years ago by
James W. MacDonald
67k • written 5.3 years ago by
salamandra
▴ 20
3
votes
3
replies
2.1k
views
Is there a way to save and open an expression set?
biobase
updated 5.3 years ago by
Kevin Blighe
★ 4.0k • written 5.3 years ago by
salamandra
▴ 20
0
votes
5
replies
2.5k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 5.6 years ago by
James W. MacDonald
67k • written 5.6 years ago by
Seymoo
• 0
2
votes
4
replies
2.9k
views
error: namespace Loading DESeq2
deseq2
error namespace
biobase
updated 6.1 years ago by
James W. MacDonald
67k • written 6.1 years ago by
jpcourneya
• 0
0
votes
2
replies
1.4k
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
6.2 years ago
cschot3
• 0
4
votes
8
replies
2.7k
views
ALL dataset, correct syntax using the exprs call?
ALL
bioconductor
biobase
exprs
updated 6.5 years ago by
Martin Morgan
25k • written 6.5 years ago by
detroit.drive
• 0
2
votes
2
replies
1.4k
views
aaMap Import "Not Available"
bioconductor
biobase
aaMap
updated 6.5 years ago by
rreck
▴ 20 • written 6.5 years ago by
detroit.drive
• 0
5
votes
7
replies
1.8k
views
Difficulty extending ExpressionSet
biobase
expressionset
eset
updated 6.5 years ago by
Martin Morgan
25k • written 6.5 years ago by
andrew.birnberg
▴ 20
2
votes
2
replies
4.9k
views
AnnotatedDataFrame is not a defined class
annotatedDataFrame
R
Biobase
10.2 years ago • updated 6.5 years ago
nonCodingGene
▴ 10
2
votes
10
replies
2.1k
views
Am I on the right tracks with a 3 factor design in Limma?
r
limma
design matrix
biobase
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
reubenmcgregor88
• 0
2
votes
2
replies
2.8k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray
biobase
6.6 years ago
charlesgwellem
▴ 10
8
votes
2
replies
3.6k
views
exprs function - clash with dplyr
exprs
dplyr
Biobase
6.7 years ago
Wolfgang Huber
★ 13k
1
vote
3
replies
1.7k
views
Boxplot and Identification of DEG
limma
biobase
geoquery
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
nia
▴ 30
2
votes
3
replies
2.0k
views
GEOquery problem in calling the function in Rstudio
R
software error
biobase
geoquery
updated 7.5 years ago by
James W. MacDonald
67k • written 7.5 years ago by
jemaatita
• 0
4
votes
3
replies
1.3k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays
expressionset
biobase
annotation
brainarray
updated 7.6 years ago by
James W. MacDonald
67k • written 7.6 years ago by
lykhenko.olexandr
• 0
0
votes
1
reply
1.3k
views
Problem Subsetting ExpressionSet
expressionset
biobase
bioconductor
updated 7.7 years ago by
James W. MacDonald
67k • written 7.7 years ago by
Tom Oates
▴ 60
1
vote
2
replies
3.4k
views
how to update feature data with different dimensions in expressionSet?
biobase
eSet
expressionSet
updated 8.2 years ago by
Martin Morgan
25k • written 8.2 years ago by
Guido Hooiveld
★ 4.1k
6
votes
13
replies
2.4k
views
Comparison of Column of AnnotatedDataFrame
biobase
AnnotatedDataFrame
8.3 years ago
Dario Strbenac
★ 1.5k
0
votes
4
replies
1.5k
views
`exprs<-` Allows setting assay data matrix size that doesn't match se.exprs
Biobase
updated 8.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.5 years ago by
psmirnov2000
• 0
1
vote
2
replies
2.7k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase
convert
sva
ringo
arrayqualitymetrics
updated 8.9 years ago by
Gordon Smyth
52k • written 8.9 years ago by
chris.rock
• 0
2
votes
2
replies
8.7k
views
Convert Expression Set into a Matrix or Data Frame
microarray
biobase
affy
R
updated 9.0 years ago by
Diego Diez
▴ 760 • written 9.0 years ago by
hshabbeer.09
• 0
0
votes
2
replies
1.6k
views
Help with annotating eset (Affy Arrays)
Biobase
annotationdbi
affy
microarray
9.2 years ago
rumroses12
• 0
2
votes
5
replies
4.1k
views
How to use t.test to select best features out of multiple features?
microarray
biobase
feature selection
t.test
R
updated 9.4 years ago by
svlachavas
▴ 840 • written 9.4 years ago by
babumanish837
▴ 10
1
vote
3
replies
3.4k
views
How to use expression set object to select genes using different gene selection methods
microarray
biobase
geoquery
updated 9.4 years ago by
svlachavas
▴ 840 • written 9.4 years ago by
babumanish837
▴ 10
0
votes
1
reply
3.3k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray
biobase
expresiondataset
r
9.4 years ago
floodking
• 0
0
votes
1
reply
6.0k
views
pvca error (Error in Data$variables : $ operator is invalid for atomic vectors)
pvca
biobase
updated 9.5 years ago by
erflynn
• 0 • written 9.8 years ago by
a.riedel
• 0
4
votes
6
replies
5.7k
views
Proper way to build phenoData object?
limma
affy
biobase
updated 10.0 years ago by
Guido Hooiveld
★ 4.1k • written 10.0 years ago by
chandlerjd58
▴ 10
1
vote
3
replies
2.7k
views
Error installing Biobase on R 3.1.2
biobase
updated 10.0 years ago by
Johannes Rainer
★ 2.1k • written 10.0 years ago by
yannick.lippi
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Prakash Sah
• 0
Thanks James!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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