Showing : biobase • reset
0
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0
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26
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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 59k • written 3 months ago by • 0
2
votes
3
replies
414
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages Biobase
updated 5 months ago by ★ 1.2k • written 5 months ago by ▴ 210
2
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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 3.5k • written 14 months ago by • 0
0
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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
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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 59k • written 17 months ago by • 0
0
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0
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278
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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 59k • written 17 months ago by • 0
1
vote
0
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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 45k • written 2.1 years ago by • 0
0
votes
0
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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 59k • written 2.6 years ago by ▴ 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 3.5k • written 2.6 years ago by ▴ 20
0
votes
5
replies
1.1k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 2.9 years ago by 59k • written 2.9 years ago by • 0
2
votes
4
replies
1.6k
views
error: namespace Loading DESeq2
deseq2 error namespace biobase
updated 3.4 years ago by 59k • written 3.4 years ago by • 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 25k • written 3.8 years ago by • 0
2
votes
2
replies
647
views
aaMap Import "Not Available"
bioconductor biobase aaMap
updated 3.8 years ago by ▴ 20 • written 3.8 years ago by • 0
5
votes
7
replies
763
views
Difficulty extending ExpressionSet
biobase expressionset eset
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 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 45k • written 3.9 years ago by • 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
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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 ★ 27k • written 4.5 years ago by ▴ 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 59k • written 4.8 years ago by • 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 59k • written 4.9 years ago by • 0
0
votes
1
reply
715
views
Problem Subsetting ExpressionSet
expressionset biobase bioconductor
updated 5.0 years ago by 59k • written 5.0 years ago by ▴ 60
1
vote
2
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2.1k
views
how to update feature data with different dimensions in expressionSet?
biobase eSet expressionSet
updated 5.6 years ago by 25k • written 5.6 years ago by ★ 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 6.5k • written 5.8 years ago by • 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 45k • written 6.2 years ago by • 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 ▴ 760 • written 6.3 years ago by • 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 ▴ 780 • written 6.7 years ago by ▴ 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 ▴ 780 • written 6.7 years ago by ▴ 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 • 0 • written 7.1 years ago by • 0
4
votes
6
replies
4.1k
views
Proper way to build phenoData object?
limma affy biobase
updated 7.3 years ago by ★ 3.2k • written 7.3 years ago by ▴ 10
1
vote
3
replies
1.8k
views
Error installing Biobase on R 3.1.2
biobase
updated 7.3 years ago by ★ 1.9k • written 7.3 years ago by • 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 1.1k • written 7.4 years ago by ▴ 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 59k • written 8.2 years ago by ▴ 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 ▴ 190 • written 8.6 years ago by 59k
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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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