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Showing :
Biobase
•
reset
0
votes
4
replies
399
views
Newbie Question - adding metadata to an analysis
Biobase
4 months ago
Bryan H
• 0
0
votes
0
replies
535
views
Job:
PhD-position in bioinformatics / computational biology
Epigenomics
NGS
Aging
Biobase
updated 11 months ago by
Michael Love
43k • written 11 months ago by
arne.sahm
• 0
3
votes
3
replies
1.2k
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
13 months ago
jacques.imbert
• 0
1
vote
4
replies
1.0k
views
Help for SeqVarData function
Biobase
SeqVarTools
21 months ago
pjuge
• 0
2
votes
4
replies
2.4k
views
Failed to install Biobase
GSVA
Biobase
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
johann.brisseau
• 0
0
votes
2
replies
1.5k
views
Automatically disconnecting database connections stored within an S4 object
DBI
S4
Biobase
updated 2.7 years ago by
Hervé Pagès
16k • written 2.8 years ago by
sandmann.t
▴ 70
0
votes
1
reply
5.0k
views
NMF installation with current R version
NMF
Biobase
updated 3.0 years ago by
shepherl
4.1k • written 3.0 years ago by
Abhishek
• 0
2
votes
1
reply
2.4k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
NGS_enthusiast
• 0
2
votes
3
replies
3.9k
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages
Biobase
updated 3.5 years ago by
ATpoint
★ 4.8k • written 3.5 years ago by
Elizabeth Purdom
▴ 210
2
votes
0
replies
870
views
PREDA shiny Golem issue
PREDAsampledata
PREDA
Biobase
3.5 years ago
Gavin
▴ 20
0
votes
2
replies
1.4k
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
3.7 years ago
sogol.bouyeh
• 0
3
votes
4
replies
2.6k
views
R session aborted: prcomp
Biobase
stats
updated 4.1 years ago by
Kevin Blighe
★ 4.0k • written 4.1 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
4.2 years ago
Daniel Brewer
▴ 100
0
votes
0
replies
1.2k
views
Job:
Senior Research Associate in Bioinformatics @ University of East Anglia - Norwich Medical School, UK
Biobase
bioinformatics
biomarkers
cancer
4.4 years ago
Daniel Brewer
▴ 100
0
votes
3
replies
1.8k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools
ReadAffy
Biobase
phenoData
affy
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
bastien_chassagnol
• 0
0
votes
0
replies
941
views
Job:
Postdoctoral Associate position to study hematopoietic neoplasms using advanced single-cell multi-omics technologies
Biobase
4.4 years ago
NamLab
• 0
0
votes
0
replies
934
views
Job:
Data analyst position to study hematopoietic neoplasms via single-cell multi-omics
Biobase
4.4 years ago
NamLab
• 0
0
votes
1
reply
949
views
Calculations (averaging and normalization) with expressionset
RTCA
Biobase
Bioconductor
expressionset
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
VanessaOak
• 0
1
vote
0
replies
1.0k
views
Job:
Computational Biologist at Denali Therapeutics
Biobase
biomarker
neuroscience
biotech
4.5 years ago
sandmann.t
▴ 70
1
vote
3
replies
1.2k
views
After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI
Biobase
4.6 years ago
Axel Klenk
★ 1.1k
4
votes
8
replies
3.2k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma
biobase
ExpressionSet
updated 5.1 years ago by
Gordon Smyth
52k • written 5.1 years ago by
sa825
• 0
0
votes
0
replies
1.2k
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error
biobase
Iranges
ArrayExpressHTS
5.2 years ago
Ed Siefker
▴ 230
0
votes
3
replies
2.2k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo
biobase
GEOquery
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
salamandra
▴ 20
3
votes
3
replies
2.2k
views
Is there a way to save and open an expression set?
biobase
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
salamandra
▴ 20
0
votes
5
replies
2.7k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
Seymoo
• 0
2
votes
4
replies
3.1k
views
error: namespace Loading DESeq2
deseq2
error namespace
biobase
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 years ago by
jpcourneya
• 0
0
votes
2
replies
1.5k
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
6.5 years ago
cschot3
• 0
4
votes
8
replies
2.9k
views
ALL dataset, correct syntax using the exprs call?
ALL
bioconductor
biobase
exprs
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
detroit.drive
• 0
2
votes
2
replies
1.5k
views
aaMap Import "Not Available"
bioconductor
biobase
aaMap
updated 6.8 years ago by
rreck
▴ 20 • written 6.8 years ago by
detroit.drive
• 0
5
votes
7
replies
2.0k
views
Difficulty extending ExpressionSet
biobase
expressionset
eset
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
andrew.birnberg
▴ 20
2
votes
2
replies
5.1k
views
AnnotatedDataFrame is not a defined class
annotatedDataFrame
R
Biobase
10.5 years ago • updated 6.8 years ago
nonCodingGene
▴ 10
2
votes
10
replies
2.3k
views
Am I on the right tracks with a 3 factor design in Limma?
r
limma
design matrix
biobase
updated 6.9 years ago by
Gordon Smyth
52k • written 6.9 years ago by
reubenmcgregor88
• 0
2
votes
2
replies
2.9k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray
biobase
6.9 years ago
charlesgwellem
▴ 20
8
votes
2
replies
3.9k
views
exprs function - clash with dplyr
exprs
dplyr
Biobase
7.0 years ago
Wolfgang Huber
★ 13k
1
vote
3
replies
1.9k
views
Boxplot and Identification of DEG
limma
biobase
geoquery
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
nia
▴ 30
2
votes
3
replies
2.2k
views
GEOquery problem in calling the function in Rstudio
R
software error
biobase
geoquery
updated 7.8 years ago by
James W. MacDonald
68k • written 7.8 years ago by
jemaatita
• 0
4
votes
3
replies
1.4k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays
expressionset
biobase
annotation
brainarray
updated 7.8 years ago by
James W. MacDonald
68k • written 7.8 years ago by
lykhenko.olexandr
• 0
0
votes
1
reply
1.4k
views
Problem Subsetting ExpressionSet
expressionset
biobase
bioconductor
updated 8.0 years ago by
James W. MacDonald
68k • written 8.0 years ago by
Tom Oates
▴ 60
1
vote
2
replies
3.6k
views
how to update feature data with different dimensions in expressionSet?
biobase
eSet
expressionSet
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
Guido Hooiveld
★ 4.1k
6
votes
13
replies
2.6k
views
Comparison of Column of AnnotatedDataFrame
biobase
AnnotatedDataFrame
8.6 years ago
Dario Strbenac
★ 1.6k
0
votes
4
replies
1.6k
views
`exprs<-` Allows setting assay data matrix size that doesn't match se.exprs
Biobase
updated 8.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.8 years ago by
psmirnov2000
• 0
1
vote
2
replies
2.9k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase
convert
sva
ringo
arrayqualitymetrics
updated 9.2 years ago by
Gordon Smyth
52k • written 9.2 years ago by
chris.rock
• 0
2
votes
2
replies
9.1k
views
Convert Expression Set into a Matrix or Data Frame
microarray
biobase
affy
R
updated 9.3 years ago by
Diego Diez
▴ 760 • written 9.3 years ago by
hshabbeer.09
• 0
0
votes
2
replies
1.7k
views
Help with annotating eset (Affy Arrays)
Biobase
annotationdbi
affy
microarray
9.5 years ago
rumroses12
• 0
2
votes
5
replies
4.2k
views
How to use t.test to select best features out of multiple features?
microarray
biobase
feature selection
t.test
R
updated 9.7 years ago by
svlachavas
▴ 840 • written 9.7 years ago by
babumanish837
▴ 10
1
vote
3
replies
3.6k
views
How to use expression set object to select genes using different gene selection methods
microarray
biobase
geoquery
updated 9.7 years ago by
svlachavas
▴ 840 • written 9.7 years ago by
babumanish837
▴ 10
0
votes
1
reply
3.5k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray
biobase
expresiondataset
r
9.7 years ago
floodking
• 0
0
votes
1
reply
6.1k
views
pvca error (Error in Data$variables : $ operator is invalid for atomic vectors)
pvca
biobase
updated 9.8 years ago by
erflynn
• 0 • written 10.1 years ago by
a.riedel
• 0
4
votes
6
replies
5.9k
views
Proper way to build phenoData object?
limma
affy
biobase
updated 10.3 years ago by
Guido Hooiveld
★ 4.1k • written 10.3 years ago by
chandlerjd58
▴ 10
1
vote
3
replies
2.8k
views
Error installing Biobase on R 3.1.2
biobase
updated 10.3 years ago by
Johannes Rainer
★ 2.1k • written 10.3 years ago by
yannick.lippi
• 0
50 results • Page
1 of 1
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Replies
Comment: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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