Showing : biobase • reset
8
votes
2
replies
3.0k
views
exprs function - clash with dplyr
exprs dplyr Biobase
6.0 years ago Wolfgang Huber ★ 13k
6
votes
13
replies
2.0k
views
Comparison of Column of AnnotatedDataFrame
biobase AnnotatedDataFrame
7.6 years ago Dario Strbenac ★ 1.5k
5
votes
7
replies
1.5k
views
Difficulty extending ExpressionSet
biobase expressionset eset
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 20
4
votes
6
replies
5.2k
views
Proper way to build phenoData object?
limma affy biobase
updated 9.3 years ago by ★ 4.0k • written 9.3 years ago by ▴ 10
4
votes
3
replies
1.2k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays expressionset biobase annotation brainarray
updated 6.9 years ago by 66k • written 6.9 years ago by • 0
4
votes
8
replies
2.3k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma biobase ExpressionSet
updated 4.1 years ago by 50k • written 4.1 years ago by • 0
4
votes
8
replies
2.4k
views
ALL dataset, correct syntax using the exprs call?
ALL bioconductor biobase exprs
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
3
votes
3
replies
1.9k
views
Is there a way to save and open an expression set?
biobase
updated 4.6 years ago by ★ 3.9k • written 4.6 years ago by ▴ 20
3
votes
3
replies
248
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
5 weeks ago • updated 4 weeks ago jacques.imbert • 0
3
votes
4
replies
2.1k
views
R session aborted: prcomp
Biobase stats
updated 3.1 years ago by ★ 3.9k • written 3.2 years ago by • 0
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 66k • written 6.8 years ago by • 0
2
votes
4
replies
1.4k
views
Failed to install Biobase
GSVA Biobase
updated 13 months ago by 66k • written 13 months ago by • 0
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 5.9 years ago by 50k • written 5.9 years ago by • 0
2
votes
2
replies
8.0k
views
Convert Expression Set into a Matrix or Data Frame
microarray biobase affy R
updated 8.3 years ago by ▴ 760 • written 8.3 years ago by • 0
2
votes
3
replies
2.0k
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages Biobase
updated 2.5 years ago by ★ 4.1k • written 2.5 years ago by ▴ 210
2
votes
2
replies
4.5k
views
AnnotatedDataFrame is not a defined class
annotatedDataFrame R Biobase
9.5 years ago • updated 5.8 years ago nonCodingGene ▴ 10
2
votes
1
reply
1.7k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 2.3 years ago by 66k • written 2.3 years ago by • 0
2
votes
4
replies
2.5k
views
error: namespace Loading DESeq2
deseq2 error namespace biobase
updated 5.4 years ago by 66k • written 5.4 years ago by • 0
2
votes
2
replies
1.2k
views
aaMap Import "Not Available"
bioconductor biobase aaMap
updated 5.8 years ago by ▴ 20 • written 5.8 years ago by • 0
2
votes
0
replies
634
views
PREDA shiny Golem issue
PREDAsampledata PREDA Biobase
2.5 years ago Gavin ▴ 20
2
votes
2
replies
2.4k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray biobase
5.9 years ago charlesgwellem ▴ 10
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 8.7 years ago by ▴ 830 • written 8.7 years ago by ▴ 10
1
vote
4
replies
622
views
Help for SeqVarData function
Biobase SeqVarTools
9 months ago pjuge • 0
1
vote
0
replies
807
views
Job: Computational Biologist at Denali Therapeutics
Biobase biomarker neuroscience biotech
3.5 years ago sandmann.t ▴ 70
1
vote
3
replies
907
views
After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI Biobase
3.6 years ago Axel Klenk ★ 1.0k
1
vote
3
replies
1.5k
views
Boxplot and Identification of DEG
limma biobase geoquery
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 30
1
vote
2
replies
3.1k
views
how to update feature data with different dimensions in expressionSet?
biobase eSet expressionSet
updated 7.6 years ago by 25k • written 7.6 years ago by ★ 4.0k
1
vote
3
replies
3.1k
views
How to use expression set object to select genes using different gene selection methods
microarray biobase geoquery
updated 8.7 years ago by ▴ 830 • written 8.7 years ago by ▴ 10
1
vote
3
replies
2.4k
views
Error installing Biobase on R 3.1.2
biobase
updated 9.3 years ago by ★ 2.0k • written 9.3 years ago by • 0
1
vote
2
replies
2.5k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase convert sva ringo arrayqualitymetrics
updated 8.2 years ago by 50k • written 8.2 years ago by • 0
0
votes
1
reply
1.2k
views
New Package: annaffy
Annotation GO rgu34a probe Biobase annaffy Annotation GO rgu34a probe Biobase annaffy
updated 21.8 years ago by ★ 2.3k • written 21.8 years ago by ▴ 20
0
votes
0
replies
901
views
Re: PDF files
Microarray Cancer Biobase affy Microarray Cancer Biobase affy
21.9 years ago Laurent Gautier ★ 2.3k
0
votes
4
replies
870
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO Biobase GO Biobase
updated 16.7 years ago by 66k • written 16.7 years ago by 25k
0
votes
1
reply
1.6k
views
Problems with url/download and http_proxy
Biobase annotate edd geneplotter tkWidgets ASSIGN Biobase annotate edd geneplotter
updated 21.9 years ago by ▴ 50 • written 21.9 years ago by ▴ 460
0
votes
2
replies
1.1k
views
Web site suggestions
Biobase edd ROC Biobase edd ROC
21.9 years ago Warnes, Gregory R ▴ 460
0
votes
1
reply
908
views
Error in .nextMethod(e1, e2) working with R2.0. in Windows
Microarray Biobase Microarray Biobase
16.7 years ago Martin Morgan 25k
0
votes
0
replies
1.2k
views
Error in xval: No Direct or Inherited Method for this call
Survival Biobase genefilter MLInterfaces Survival Biobase genefilter MLInterfaces
17.6 years ago Martin Morgan 25k
0
votes
1
reply
937
views
installation problems
Biobase Biobase
updated 22.0 years ago by ★ 2.3k • written 22.0 years ago by ▴ 120
0
votes
1
reply
1.1k
views
biobase
Biobase affy Biobase affy
updated 22.1 years ago by ▴ 150 • written 22.1 years ago by ▴ 70
0
votes
0
replies
1.0k
views
Does anyone have the same problem with new("ExpressionSet", ...) ?
Annotation Biobase Annotation Biobase
16.7 years ago Martin Morgan 25k
0
votes
1
reply
1.0k
views
Biobase version 1.0 on windows XP...
Biobase Biobase
updated 22.1 years ago by ▴ 530 • written 22.1 years ago by ▴ 90
0
votes
0
replies
1.5k
views
peer review process/DATE CORRECTION
Biobase annotate edd genefilter geneplotter rhdf5 multtest ROC tkWidgets affy AnnBuilder
22.1 years ago Vincent J. Carey, Jr. 6.7k
0
votes
9
replies
1.9k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 17.0 years ago by ★ 7.4k • written 17.0 years ago by ★ 2.2k
0
votes
4
replies
1.1k
views
Communicating gene-probe relationships to sam
SNP Biobase siggenes SNP Biobase siggenes
18.1 years ago Charles Crane ▴ 30
0
votes
0
replies
854
views
ABPkgBuilder Error; Again
Annotation GO Cancer Organism Biobase annotate AnnBuilder PROcess Annotation GO Cancer
18.8 years ago Barry Henderson ▴ 250
0
votes
1
reply
1.1k
views
Problems accessing the Milan package through the vignettes Explorer
Cancer Biobase annotate edd geneplotter multtest tkWidgets affydata vsn graph hexbin
updated 21.0 years ago by ★ 2.9k • written 21.0 years ago by ▴ 130
0
votes
1
reply
664
views
Biobase/reposTools Dependency
Biobase reposTools Biobase reposTools
updated 20.9 years ago by ★ 5.5k • written 20.9 years ago by ▴ 220
0
votes
0
replies
858
views
Error Installation for Genefilter
Biobase genefilter Biobase genefilter
20.9 years ago Lisa Devereaux ▴ 20
0
votes
1
reply
797
views
Problems
Biobase reposTools Biobase reposTools
updated 20.9 years ago by ★ 5.5k • written 20.9 years ago by ▴ 10
0
votes
1
reply
798
views
Difficulty in installing Biobase 1.3.22
GO Biobase GO Biobase
updated 21.0 years ago by ★ 3.9k • written 21.0 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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