Showing : Oligo • reset
0
votes
4
replies
369
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
5 weeks ago • updated 4 weeks ago Efra • 0
0
votes
2
replies
365
views
Error Oligo package asking for pd.2.0 package annotation
oligo
updated 4 months ago by ★ 3.9k • written 4 months ago by • 0
2
votes
1
reply
663
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 9 months ago by 65k • written 9 months ago by • 0
1
vote
4
replies
657
views
How to annotate mir4.1 arrays?
AffymetrixChip miRNA oligo
11 months ago • updated 8 months ago richardallenfriedmanbrooklyn ▴ 20
0
votes
1
reply
584
views
Can't make a boxplot or hist with oligo
oligo
updated 12 months ago by 65k • written 12 months ago by • 0
0
votes
1
reply
462
views
I need the pd.cytoscanhd.array.
oligo
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
5
replies
1.1k
views
oligo rma() background normalization crash in basicRMA()
basicRMA crash rma oligo
14 months ago Steffen Moeller ▴ 90
1
vote
6
replies
1.4k
views
How to annotate Data with oligo and Affymetrix HuGene-2_0-st package?
oligo
updated 19 months ago by 65k • written 19 months ago by • 0
2
votes
2
replies
857
views
How to compute P/A calls at gene-level probeset of Human Gene 1.0 ST Array
pd.hugene.1.0.st.v1 oligo AffymetrixChip
22 months ago Yang Shi ▴ 10
2
votes
5
replies
1.1k
views
Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1 oligo AffymetrixChip
23 months ago • updated 22 months ago Yang Shi ▴ 10
2
votes
4
replies
1.1k
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219 oligo AffymetrixChip
23 months ago Yang Shi ▴ 10
4
votes
10
replies
1.9k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
23 months ago Yang Shi ▴ 10
3
votes
4
replies
1.6k
views
Quantile Normalization after rma or not?
limma Microarray oligo
23 months ago Yang Shi ▴ 10
2
votes
2
replies
795
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
23 months ago Yang Shi ▴ 10
1
vote
2
replies
1.0k
views
oligo package blas error
rma openblas blas oligo
2.6 years ago ch_el ▴ 10
0
votes
1
reply
628
views
Clariom-D array - subsetting probes to known genes prior to normalization
oligo
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 10
1
vote
16
replies
3.4k
views
cant read celfiles using oligo package
oligo
2.7 years ago scipio04 • 0
2
votes
8
replies
1.2k
views
pdInfoBuilder created problematic package for Affymetrix chip tiling array
oligoClasses oligo pdInfoBuilder
2.8 years ago • updated 2.7 years ago efoss ▴ 10
2
votes
1
reply
2.8k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO oligo
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.2 years ago by • 0
2
votes
5
replies
1.7k
views
Summarize Microarray data on a transcript level
pd.clariom.d.human oligo clariomdhumanprobeset.db
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
0
votes
2
replies
1.3k
views
Annotation clariom D microarray
clariomdhumantranscriptcluster.db oligo
3.5 years ago Luca • 0
0
votes
2
replies
1.3k
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
3.5 years ago Luca • 0
0
votes
1
reply
830
views
Plot legend with oligo::hist()
oligo
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 10
1
vote
1
reply
774
views
Is it possible to run arrayQualitymetrics or some similar package on a HTAFeatureSet?
arrayQualityMetrics oligo
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 10
2
votes
3
replies
1.1k
views
Annotation package generation for HTA-2_0 by pdInfoBuilder fails
microarray pdInfoBuilder oligo
updated 3.8 years ago by 65k • written 3.8 years ago by • 0
0
votes
1
reply
919
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
0
votes
1
reply
579
views
normalized multiple microarrays with different design files oligo
microarray oligo
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
0
votes
2
replies
1.0k
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy rma frma oligo
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
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
2
replies
2.3k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 20
0
votes
1
reply
1.7k
views
R: oligo packages install error
oligo packages error
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
1
vote
2
replies
1.4k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 4.8 years ago by 65k • written 4.8 years ago by ★ 3.9k
2
votes
4
replies
1.5k
views
rma summarization error when normalizing using oligo and brainarray cdf
oligo brainarray mbni
4.8 years ago Moosa • 0
0
votes
3
replies
988
views
Brainarray CDF with oligopackage
Brainarray CDF oligo
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 50
1
vote
5
replies
1.2k
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 830
0
votes
0
replies
795
views
run OLIGO package encounters errors:
oligo
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
3
votes
4
replies
2.9k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 4.2 years ago by • 0 • written 5.3 years ago by • 0
0
votes
1
reply
1.3k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 4.4 years ago by • 0 • written 5.3 years ago by ★ 3.9k
0
votes
5
replies
1.8k
views
Annotating Expression Set for GSVA w/ Brainarray Human Gene 1.1 ST Array CDF
bioconductor brainarray genefilter oligo
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
1.1k
views
Error: 'unknown input format' while trying http://bioconductor.org/packages/3.7/bioc
error oligo affy
5.9 years ago kritikamish99 ▴ 10
0
votes
1
reply
1.0k
views
Making microarray probeset presence/absence calls
oligo
updated 6.2 years ago by 65k • written 6.2 years ago by ▴ 70
0
votes
2
replies
1.3k
views
error message from oligo package
oligo
updated 2.7 years ago by • 0 • written 6.3 years ago by • 0
1
vote
3
replies
4.2k
views
How to select top 10% highly variable genes in microarray data?
r microarray snp6.0 oligo
updated 6.3 years ago by ▴ 350 • written 6.3 years ago by ▴ 110
1
vote
0
replies
1.4k
views
Problems running oligo functions in parallel on a linux computer
biocparallel oligo rma linux parallel
6.3 years ago s.munster ▴ 40
0
votes
4
replies
6.5k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
6.4 years ago llkxiaolan ▴ 10
0
votes
7
replies
4.3k
views
How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip
annotation oligo
updated 6.4 years ago by ★ 3.9k • written 6.4 years ago by ▴ 10
1
vote
6
replies
1.7k
views
oligo: crash/segfault when fitting probelevel model
oligo openblas preprocessCore
updated 6.7 years ago by 65k • written 6.7 years ago by ★ 3.9k
0
votes
2
replies
1.9k
views
Reading CEL files using Oligo and pd.hta.2.0 packages in Windows 7
oligo pd.hta.2.0 CEL R windows 7
6.7 years ago ladhikari • 0
0
votes
2
replies
1.2k
views
oligo and parallel computing (on Windows)?
oligo parallel computation
updated 6.7 years ago by 65k • written 6.7 years ago by ★ 3.9k
50 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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