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biobase
•
reset
0
votes
0
replies
26
views
NMF installation with current R version
NMF
Biobase
10 days ago
Abhishek
• 0
2
votes
1
reply
278
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 3 months ago by
James W. MacDonald
59k • written 3 months ago by
NGS_enthusiast
• 0
2
votes
3
replies
414
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages
Biobase
updated 5 months ago by
ATpoint
★ 1.2k • written 5 months ago by
Elizabeth Purdom
▴ 210
2
votes
0
replies
157
views
PREDA shiny Golem issue
PREDAsampledata
PREDA
Biobase
6 months ago
Gavin
▴ 20
0
votes
2
replies
325
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
8 months ago
sogol.bouyeh
• 0
3
votes
4
replies
840
views
R session aborted: prcomp
Biobase
stats
updated 13 months ago by
Kevin Blighe
3.5k • written 14 months ago by
Gero
• 0
0
votes
0
replies
271
views
Job:
Cancer Bioinformatician @ University of East Anglia - Norwich Medical School, UK
cancer
postdoc
biomarkers
Biobase
14 months ago
Daniel Brewer
▴ 90
0
votes
0
replies
361
views
Job:
Senior Research Associate in Bioinformatics @ University of East Anglia - Norwich Medical School, UK
Biobase
bioinformatics
biomarkers
cancer
17 months ago
Daniel Brewer
▴ 90
0
votes
3
replies
533
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools
ReadAffy
Biobase
phenoData
affy
updated 17 months ago by
James W. MacDonald
59k • written 17 months ago by
bastien_chassagnol
• 0
0
votes
0
replies
278
views
Job:
Postdoctoral Associate position to study hematopoietic neoplasms using advanced single-cell multi-omics technologies
Biobase
17 months ago
NamLab
• 0
0
votes
0
replies
272
views
Job:
Data analyst position to study hematopoietic neoplasms via single-cell multi-omics
Biobase
17 months ago
NamLab
• 0
0
votes
1
reply
279
views
Calculations (averaging and normalization) with expressionset
RTCA
Biobase
Bioconductor
expressionset
updated 17 months ago by
James W. MacDonald
59k • written 17 months ago by
VanessaOak
• 0
1
vote
0
replies
335
views
Job:
Computational Biologist at Denali Therapeutics
Biobase
biomarker
neuroscience
biotech
17 months ago
sandmann.t
▴ 70
1
vote
3
replies
426
views
After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI
Biobase
19 months ago
Axel Klenk
▴ 990
4
votes
8
replies
957
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma
biobase
ExpressionSet
updated 2.1 years ago by
Gordon Smyth
45k • written 2.1 years ago by
sa825
• 0
0
votes
0
replies
281
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error
biobase
Iranges
ArrayExpressHTS
2.2 years ago
Ed Siefker
▴ 230
0
votes
3
replies
793
views
When applying rma to featureset get error: 'package' must be of length 1
oligo
biobase
GEOquery
updated 2.6 years ago by
James W. MacDonald
59k • written 2.6 years ago by
salamandra
▴ 20
3
votes
3
replies
945
views
Is there a way to save and open an expression set?
biobase
updated 2.6 years ago by
Kevin Blighe
3.5k • written 2.6 years ago by
salamandra
▴ 20
0
votes
5
replies
1.1k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 2.9 years ago by
James W. MacDonald
59k • written 2.9 years ago by
Seymoo
• 0
2
votes
4
replies
1.6k
views
error: namespace Loading DESeq2
deseq2
error namespace
biobase
updated 3.4 years ago by
James W. MacDonald
59k • written 3.4 years ago by
jpcourneya
• 0
0
votes
2
replies
630
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
3.5 years ago
cschot3
• 0
4
votes
8
replies
1.4k
views
ALL dataset, correct syntax using the exprs call?
ALL
bioconductor
biobase
exprs
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
detroit.drive
• 0
2
votes
2
replies
647
views
aaMap Import "Not Available"
bioconductor
biobase
aaMap
updated 3.8 years ago by
rreck
▴ 20 • written 3.8 years ago by
detroit.drive
• 0
5
votes
7
replies
763
views
Difficulty extending ExpressionSet
biobase
expressionset
eset
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
andrew.birnberg
▴ 20
2
votes
2
replies
3.0k
views
AnnotatedDataFrame is not a defined class
annotatedDataFrame
R
Biobase
7.5 years ago • updated 3.8 years ago
nonCodingGene
▴ 10
2
votes
10
replies
839
views
Am I on the right tracks with a 3 factor design in Limma?
r
limma
design matrix
biobase
updated 3.9 years ago by
Gordon Smyth
45k • written 3.9 years ago by
reubenmcgregor88
• 0
2
votes
2
replies
1.2k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray
biobase
3.9 years ago
charlesgwellem
▴ 10
8
votes
2
replies
1.7k
views
exprs function - clash with dplyr
exprs
dplyr
Biobase
4.0 years ago
Wolfgang Huber
13k
1
vote
3
replies
847
views
Boxplot and Identification of DEG
limma
biobase
geoquery
updated 4.5 years ago by
Aaron Lun
★ 27k • written 4.5 years ago by
nia
▴ 30
2
votes
3
replies
1.2k
views
GEOquery problem in calling the function in Rstudio
R
software error
biobase
geoquery
updated 4.8 years ago by
James W. MacDonald
59k • written 4.8 years ago by
jemaatita
• 0
4
votes
3
replies
743
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays
expressionset
biobase
annotation
brainarray
updated 4.9 years ago by
James W. MacDonald
59k • written 4.9 years ago by
lykhenko.olexandr
• 0
0
votes
1
reply
715
views
Problem Subsetting ExpressionSet
expressionset
biobase
bioconductor
updated 5.0 years ago by
James W. MacDonald
59k • written 5.0 years ago by
Tom Oates
▴ 60
1
vote
2
replies
2.1k
views
how to update feature data with different dimensions in expressionSet?
biobase
eSet
expressionSet
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
Guido Hooiveld
★ 3.2k
6
votes
13
replies
1.2k
views
Comparison of Column of AnnotatedDataFrame
biobase
AnnotatedDataFrame
5.6 years ago
Dario Strbenac
★ 1.5k
0
votes
4
replies
760
views
`exprs<-` Allows setting assay data matrix size that doesn't match se.exprs
Biobase
updated 5.7 years ago by
Kasper Daniel Hansen
6.5k • written 5.8 years ago by
psmirnov2000
• 0
1
vote
2
replies
1.7k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase
convert
sva
ringo
arrayqualitymetrics
updated 6.2 years ago by
Gordon Smyth
45k • written 6.2 years ago by
chris.rock
• 0
2
votes
2
replies
6.1k
views
Convert Expression Set into a Matrix or Data Frame
microarray
biobase
affy
R
updated 6.3 years ago by
Diego Diez
▴ 760 • written 6.3 years ago by
hshabbeer.09
• 0
0
votes
2
replies
987
views
Help with annotating eset (Affy Arrays)
Biobase
annotationdbi
affy
microarray
6.5 years ago
rumroses12
• 0
2
votes
5
replies
3.1k
views
How to use t.test to select best features out of multiple features?
microarray
biobase
feature selection
t.test
R
updated 6.7 years ago by
svlachavas
▴ 780 • written 6.7 years ago by
babumanish837
▴ 10
1
vote
3
replies
2.1k
views
How to use expression set object to select genes using different gene selection methods
microarray
biobase
geoquery
updated 6.7 years ago by
svlachavas
▴ 780 • written 6.7 years ago by
babumanish837
▴ 10
0
votes
1
reply
2.3k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray
biobase
expresiondataset
r
6.7 years ago
floodking
• 0
0
votes
1
reply
5.1k
views
pvca error (Error in Data$variables : $ operator is invalid for atomic vectors)
pvca
biobase
updated 6.8 years ago by
erflynn
• 0 • written 7.1 years ago by
a.riedel
• 0
4
votes
6
replies
4.1k
views
Proper way to build phenoData object?
limma
affy
biobase
updated 7.3 years ago by
Guido Hooiveld
★ 3.2k • written 7.3 years ago by
chandlerjd58
▴ 10
1
vote
3
replies
1.8k
views
Error installing Biobase on R 3.1.2
biobase
updated 7.3 years ago by
Johannes Rainer
★ 1.9k • written 7.3 years ago by
yannick.lippi
• 0
0
votes
2
replies
820
views
How to Represent Data from Various Different Assays in a Single Class?
biobase
updated 7.4 years ago by
Levi Waldron
1.1k • written 7.4 years ago by
cannin
▴ 20
0
votes
3
replies
1.1k
views
conflict in names between phenoData and protocolData during RMA
biobase
7.5 years ago
bin.shan
• 0
0
votes
0
replies
1.0k
views
easyRNASeq: Number of total counts
GeneExpression
RNASeq
Genetics
Coverage
Normalization
BSgenome
Biobase
Biostrings
biomaRt
8.1 years ago
Guest User
★ 12k
0
votes
2
replies
1.6k
views
make.cdf.package Error in copySubstitute
GO
cdf
Biobase
affy
GO
cdf
Biobase
affy
updated 8.2 years ago by
James W. MacDonald
59k • written 8.2 years ago by
matthew vitalone
▴ 30
0
votes
0
replies
643
views
Problem with the oligo package for nimblegen analysis
Biobase
Biobase
8.6 years ago
William Oldham
▴ 10
0
votes
1
reply
1.3k
views
Coercing matrix into expression set, for normalization of only subsets of miRNAs (affy miRNA3.0)
miRNA
Normalization
GO
Biobase
affy
convert
oligo
miRNA
Normalization
GO
Biobase
affy
updated 8.6 years ago by
Pekka Kohonen
▴ 190 • written 8.6 years ago by
James W. MacDonald
59k
50 results • Page
1 of 1
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Replies
Comment: performing the differential binding in ChIP-seq
by
ATpoint
★ 1.2k
Cross-posted https://www.biostars.org/p/9524012/#9524012
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
Yes, i tried that. I used salmon bootstraps also for the same RNAseq data to run Swish and performed the Differential transcript expressio…
Comment: how to make a group to apply the data to CAMERA
by
Akira
• 0
Thank you so much for your quick answer!! I will look into them! I appreciate your kind support.
Comment: performing the differential binding in ChIP-seq
by
Bogdan
▴ 640
I am asking the question because we have two sets of ChIP-seq data for a histone mark (lets' say H3K4me1) that were generated with : <> an…
Comment: performing the differential binding in ChIP-seq
by
Bogdan
▴ 640
Thank you. Yes, DiffBind might be a good choice shall we have replicates per sample. Another choice is MA-norm2. Any other well-tested sug…
Votes
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
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Gordon Smyth
45k
Popular Question
to
andrebolerbarros
▴ 10
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to
James W. MacDonald
59k
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to
Guido Hooiveld
★ 3.2k
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to
Kevin Blighe
3.5k
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