Showing : Biobase • reset
3
votes
3
replies
250
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
5 weeks ago • updated 4 weeks ago jacques.imbert • 0
1
vote
4
replies
624
views
Help for SeqVarData function
Biobase SeqVarTools
9 months ago pjuge • 0
2
votes
4
replies
1.4k
views
Failed to install Biobase
GSVA Biobase
updated 14 months ago by 66k • written 14 months ago by • 0
0
votes
2
replies
1.0k
views
Automatically disconnecting database connections stored within an S4 object
DBI S4 Biobase
updated 21 months ago by 16k • written 21 months ago by ▴ 70
0
votes
1
reply
3.0k
views
NMF installation with current R version
NMF Biobase
updated 24 months ago by 3.9k • written 2.0 years ago by • 0
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
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
0
replies
634
views
PREDA shiny Golem issue
PREDAsampledata PREDA Biobase
2.5 years ago Gavin ▴ 20
0
votes
2
replies
993
views
Gene expression in R
limma edgeR Biobase GeneExpression
2.7 years ago sogol.bouyeh • 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
0
votes
0
replies
868
views
Job: Cancer Bioinformatician @ University of East Anglia - Norwich Medical School, UK
cancer postdoc biomarkers Biobase
3.2 years ago Daniel Brewer ▴ 100
0
votes
0
replies
924
views
Job: Senior Research Associate in Bioinformatics @ University of East Anglia - Norwich Medical School, UK
Biobase bioinformatics biomarkers cancer
3.4 years ago Daniel Brewer ▴ 100
0
votes
3
replies
1.4k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 3.4 years ago by 66k • written 3.4 years ago by • 0
0
votes
0
replies
705
views
Job: Postdoctoral Associate position to study hematopoietic neoplasms using advanced single-cell multi-omics technologies
Biobase
3.4 years ago NamLab • 0
0
votes
0
replies
695
views
Job: Data analyst position to study hematopoietic neoplasms via single-cell multi-omics
Biobase
3.4 years ago NamLab • 0
0
votes
1
reply
701
views
Calculations (averaging and normalization) with expressionset
RTCA Biobase Bioconductor expressionset
updated 3.5 years ago by 66k • written 3.5 years ago by • 0
1
vote
0
replies
808
views
Job: Computational Biologist at Denali Therapeutics
Biobase biomarker neuroscience biotech
3.5 years ago sandmann.t ▴ 70
1
vote
3
replies
912
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
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
0
votes
0
replies
889
views
No methods found in package Biobase for request: read.AnnotatedDataFrame
software error biobase Iranges ArrayExpressHTS
4.2 years ago Ed Siefker ▴ 230
0
votes
3
replies
1.7k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 4.6 years ago by 66k • written 4.6 years ago by ▴ 20
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
0
votes
5
replies
2.1k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 4.9 years ago by 66k • written 4.9 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
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
5.5 years ago cschot3 • 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
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
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
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
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
2.4k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray biobase
5.9 years ago charlesgwellem ▴ 10
8
votes
2
replies
3.1k
views
exprs function - clash with dplyr
exprs dplyr Biobase
6.0 years ago Wolfgang Huber ★ 13k
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
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
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
0
votes
1
reply
1.1k
views
Problem Subsetting ExpressionSet
expressionset biobase bioconductor
updated 7.0 years ago by 66k • written 7.0 years ago by ▴ 60
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
6
votes
13
replies
2.0k
views
Comparison of Column of AnnotatedDataFrame
biobase AnnotatedDataFrame
7.6 years ago Dario Strbenac ★ 1.5k
0
votes
4
replies
1.3k
views
`exprs<-` Allows setting assay data matrix size that doesn't match se.exprs
Biobase
updated 7.7 years ago by ★ 6.5k • written 7.8 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
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
0
votes
2
replies
1.4k
views
Help with annotating eset (Affy Arrays)
Biobase annotationdbi affy microarray
8.5 years ago rumroses12 • 0
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
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
0
votes
1
reply
3.1k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray biobase expresiondataset r
8.7 years ago floodking • 0
0
votes
1
reply
5.8k
views
pvca error (Error in Data$variables : $ operator is invalid for atomic vectors)
pvca biobase
updated 8.8 years ago by • 0 • written 9.1 years ago by • 0
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
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
0
votes
2
replies
1.3k
views
How to Represent Data from Various Different Assays in a Single Class?
biobase
updated 9.4 years ago by ★ 1.1k • written 9.4 years ago by ▴ 20
0
votes
3
replies
1.6k
views
conflict in names between phenoData and protocolData during RMA
biobase
9.6 years ago bin.shan • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf by James W. MacDonald 66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf by Brandon • 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Comment: Slightly different count plots from R and spreadsheet by Michael Love 42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM by Vitor • 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). !…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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