Showing : Biobase • reset
3
votes
3
replies
200
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
22 days ago • updated 16 days ago jacques.imbert • 0
1
vote
4
replies
597
views
Help for SeqVarData function
Biobase SeqVarTools
8 months ago pjuge • 0
2
votes
4
replies
1.4k
views
Failed to install Biobase
GSVA Biobase
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
2
replies
1.0k
views
Automatically disconnecting database connections stored within an S4 object
DBI S4 Biobase
updated 20 months ago by 16k • written 20 months ago by ▴ 70
0
votes
1
reply
2.9k
views
NMF installation with current R version
NMF Biobase
updated 23 months ago by 3.9k • written 24 months 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 65k • 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 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 210
2
votes
0
replies
622
views
PREDA shiny Golem issue
PREDAsampledata PREDA Biobase
2.5 years ago Gavin ▴ 20
0
votes
2
replies
961
views
Gene expression in R
limma edgeR Biobase GeneExpression
2.7 years ago • updated 2.6 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 3.1 years ago by • 0
0
votes
0
replies
856
views
Job: Cancer Bioinformatician @ University of East Anglia - Norwich Medical School, UK
cancer postdoc biomarkers Biobase
3.1 years ago Daniel Brewer ▴ 100
0
votes
0
replies
907
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 65k • written 3.4 years ago by • 0
0
votes
0
replies
692
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
682
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
687
views
Calculations (averaging and normalization) with expressionset
RTCA Biobase Bioconductor expressionset
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
1
vote
0
replies
798
views
Job: Computational Biologist at Denali Therapeutics
Biobase biomarker neuroscience biotech
3.4 years ago sandmann.t ▴ 70
1
vote
3
replies
894
views
After the Support Site upgrade: how can I order posts by creation (not reply) time?
SupportSiteUI Biobase
3.5 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 4.0 years ago by 50k • written 4.0 years ago by • 0
0
votes
0
replies
882
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 4.5 years ago by 65k • written 4.5 years ago by ▴ 20
3
votes
3
replies
1.8k
views
Is there a way to save and open an expression set?
biobase
updated 4.5 years ago by ★ 3.9k • written 4.5 years ago by ▴ 20
0
votes
5
replies
2.1k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 4.8 years ago by 65k • written 4.8 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 65k • written 5.4 years ago by • 0
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
5.4 years ago cschot3 • 0
4
votes
8
replies
2.3k
views
ALL dataset, correct syntax using the exprs call?
ALL bioconductor biobase exprs
updated 5.7 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
4.4k
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 5.8 years ago by 50k • written 5.8 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
3.0k
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 65k • 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 6.8 years ago by 65k • written 6.8 years ago by • 0
0
votes
1
reply
1.1k
views
Problem Subsetting ExpressionSet
expressionset biobase bioconductor
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 60
1
vote
2
replies
3.0k
views
how to update feature data with different dimensions in expressionSet?
biobase eSet expressionSet
updated 7.5 years ago by 25k • written 7.5 years ago by ★ 3.9k
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 7.7 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 8.1 years ago by 50k • written 8.2 years ago by • 0
2
votes
2
replies
7.9k
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 8.6 years ago by ▴ 830 • written 8.6 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
3.0k
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 8.7 years ago by • 0 • written 9.0 years ago by • 0
4
votes
6
replies
5.2k
views
Proper way to build phenoData object?
limma affy biobase
updated 9.2 years ago by ★ 3.9k • written 9.2 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
1.5k
views
conflict in names between phenoData and protocolData during RMA
biobase
9.5 years ago bin.shan • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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