Showing : Oligo • reset
2
votes
4
replies
87
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219 oligo AffymetrixChip
3 days ago Yang Shi • 0
4
votes
10
replies
192
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
4 days ago • updated 3 days ago Yang Shi • 0
3
votes
4
replies
118
views
Quantile Normalization after rma or not?
limma Microarray oligo
4 days ago Yang Shi • 0
2
votes
2
replies
79
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
6 days ago Yang Shi • 0
1
vote
2
replies
261
views
oligo package blas error
rma openblas blas oligo
8 months ago ch_el ▴ 10
0
votes
1
reply
180
views
Clariom-D array - subsetting probes to known genes prior to normalization
oligo
updated 9 months ago by 59k • written 9 months ago by ▴ 10
1
vote
16
replies
855
views
cant read celfiles using oligo package
oligo
9 months ago scipio04 • 0
2
votes
8
replies
408
views
pdInfoBuilder created problematic package for Affymetrix chip tiling array
oligoClasses oligo pdInfoBuilder
10 months ago • updated 9 months ago efoss ▴ 10
2
votes
1
reply
610
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO oligo
updated 14 months ago by 59k • written 14 months ago by • 0
0
votes
2
replies
483
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
updated 15 months ago by 25k • written 15 months ago by • 0
2
votes
5
replies
631
views
Summarize Microarray data on a transcript level
pd.clariom.d.human oligo clariomdhumanprobeset.db
updated 17 months ago by 59k • written 17 months ago by • 0
5
votes
8
replies
1.6k
views
how to annotate arrays
affy annotation microarray oligo
updated 17 months ago by 59k • written 6.8 years ago by • 0
0
votes
2
replies
415
views
Annotation clariom D microarray
clariomdhumantranscriptcluster.db oligo
18 months ago luca.piacentini • 0
0
votes
2
replies
453
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
18 months ago luca.piacentini • 0
0
votes
1
reply
332
views
Plot legend with oligo::hist()
oligo
updated 19 months ago by 59k • written 19 months ago by • 0
1
vote
1
reply
284
views
Is it possible to run arrayQualitymetrics or some similar package on a HTAFeatureSet?
arrayQualityMetrics oligo
updated 19 months ago by 59k • written 19 months ago by • 0
2
votes
3
replies
428
views
Annotation package generation for HTA-2_0 by pdInfoBuilder fails
microarray pdInfoBuilder oligo
updated 22 months ago by 59k • written 22 months ago by • 0
0
votes
1
reply
325
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 2.1 years ago by 59k • written 2.1 years ago by • 0
3
votes
4
replies
1.4k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 2.3 years ago by • 0 • written 3.4 years ago by • 0
0
votes
1
reply
208
views
normalized multiple microarrays with different design files oligo
microarray oligo
updated 2.3 years ago by 59k • written 2.3 years ago by • 0
0
votes
1
reply
651
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 2.5 years ago by • 0 • written 3.4 years ago by ★ 3.2k
0
votes
2
replies
494
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy rma frma oligo
updated 2.5 years ago by 59k • written 2.5 years ago by • 0
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
2
votes
2
replies
997
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 2.6 years ago by 59k • written 2.6 years ago by ▴ 20
0
votes
1
reply
819
views
R: oligo packages install error
oligo packages error
updated 2.9 years ago by 25k • written 2.9 years ago by • 0
1
vote
2
replies
578
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 2.9 years ago by 59k • written 2.9 years ago by ★ 3.2k
2
votes
4
replies
709
views
rma summarization error when normalizing using oligo and brainarray cdf
oligo brainarray mbni
2.9 years ago Moosa • 0
0
votes
3
replies
445
views
Brainarray CDF with oligopackage
Brainarray CDF oligo
updated 3.0 years ago by 59k • written 3.0 years ago by ▴ 20
1
vote
5
replies
493
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 3.2 years ago by 59k • written 3.2 years ago by ▴ 780
0
votes
0
replies
343
views
run OLIGO package encounters errors:
oligo
updated 3.2 years ago by 25k • written 3.2 years ago by • 0
0
votes
11
replies
2.4k
views
SNP6 data to VCF
SNP oligo ASSIGN SNP oligo ASSIGN
updated 3.7 years ago by • 0 • written 10.3 years ago by 21k
0
votes
5
replies
1.0k
views
Annotating Expression Set for GSVA w/ Brainarray Human Gene 1.1 ST Array CDF
bioconductor brainarray genefilter oligo
updated 4.0 years ago by 59k • written 4.0 years ago by • 0
0
votes
1
reply
583
views
Error: 'unknown input format' while trying http://bioconductor.org/packages/3.7/bioc
error oligo affy
4.0 years ago kritikamish99 ▴ 10
0
votes
8
replies
2.7k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 4.2 years ago by • 0 • written 8.3 years ago by ▴ 300
0
votes
1
reply
605
views
Making microarray probeset presence/absence calls
oligo
updated 4.3 years ago by 59k • written 4.3 years ago by ▴ 60
0
votes
2
replies
710
views
error message from oligo package
oligo
updated 9 months ago by • 0 • written 4.4 years ago by • 0
0
votes
3
replies
2.6k
views
How to select top 10% highly variable genes in microarray data?
r microarray snp6.0 oligo
updated 4.4 years ago by ▴ 270 • written 4.4 years ago by ▴ 90
1
vote
0
replies
796
views
Problems running oligo functions in parallel on a linux computer
biocparallel oligo rma linux parallel
4.4 years ago s.munster ▴ 40
0
votes
4
replies
3.6k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
4.5 years ago llkxiaolan • 0
0
votes
7
replies
2.7k
views
How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip
annotation oligo
updated 4.5 years ago by ★ 3.2k • written 4.5 years ago by • 0
1
vote
6
replies
1.1k
views
oligo: crash/segfault when fitting probelevel model
oligo openblas preprocessCore
updated 4.7 years ago by 59k • written 4.7 years ago by ★ 3.2k
0
votes
2
replies
1.1k
views
Reading CEL files using Oligo and pd.hta.2.0 packages in Windows 7
oligo pd.hta.2.0 CEL R windows 7
4.7 years ago ladhikari • 0
0
votes
2
replies
837
views
oligo and parallel computing (on Windows)?
oligo parallel computation
updated 4.8 years ago by 59k • written 4.8 years ago by ★ 3.2k
5
votes
6
replies
1.4k
views
Error installing pd.huex.1.0.st.v2: database disk image is malformed
pd.huex.1.0.st.v2 oligo
updated 4.8 years ago by 59k • written 4.8 years ago by ★ 3.2k
2
votes
2
replies
625
views
paCalls with Clariom Chips
oligo microarray clariom
updated 4.8 years ago by 59k • written 4.8 years ago by • 0
6
votes
8
replies
1.4k
views
Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
affy aroma.affymetrix exon array xps oligo
4.9 years ago Gordon Smyth 45k
3
votes
1
reply
856
views
Filtering absent transcripts from Gene ST array
microarray oligo gene ST pacalls
updated 5.1 years ago by 59k • written 5.1 years ago by • 0
0
votes
1
reply
930
views
oligo rma() function giving unused argument error
oligo rma
updated 5.1 years ago by 59k • written 5.1 years ago by ▴ 40
1
vote
4
replies
2.2k
views
Error with boxplot command from oligo package with raw Affy data
oligo
updated 5.1 years ago by 59k • written 5.1 years ago by • 0
2
votes
3
replies
1.1k
views
Problem with memory limit in Rstudio/Windows when importing Affymetrix HTA 2.0 CEL files with oligo R package
oligo hta2.0 affymetrix microarrays memory problem
updated 5.1 years ago by 59k • written 5.1 years ago by ▴ 780
50 results • Page 1 of 1
Recent ...
Replies
Answer: regression analysis for epic array methylation data using limma by Basti ▴ 280
Which package do you intend to use ? There are many tutorials in packages vignette that show you how to perform differential methylation an…
Comment: scRNASeq reference at a transcript level by Basti ▴ 280
I believe this question is not related to any Bioconductor package, I think the only solution to this question is to search yourself in Pub…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Upgrading the package solved the issue, thanks!
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by ATpoint ★ 1.2k
The error comes from the `mixsqp` package, see https://github.com/stephens999/ashr/issues/131. Upgrading the package to the most recent 0.3…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Thanks for the suggestion. I ran the following filtering criteria: ``` keep <- rowSums(counts(dds) >= 10) >= 5 dds <- dds[keep,] ``` It ga…
Votes
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: UniprotKB AC/ID to Entrez ID Conversion
edgeR: what to do with no replicates
Differential gene expression anlaysis?
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