Showing : oligo • reset
0
votes
1
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239
views
Custom CDF creation for HTA 2.0 array using GTF annotation
oligo oligoClasses pdInfoBuilder affycoretools affyio
20 days ago • updated 19 days ago Seymoo • 0
1
vote
9
replies
1.5k
views
Cannot install oligo on Fedora
oligo source Install
11 months ago • updated 10 months ago Guido Hooiveld ★ 4.1k
0
votes
4
replies
853
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
13 months ago Efra • 0
0
votes
2
replies
945
views
Error Oligo package asking for pd.2.0 package annotation
oligo
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
0
votes
3
replies
2.2k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 4.2 years ago by • 0
0
votes
5
replies
2.4k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 11.3 years ago by ★ 13k
1
vote
5
replies
2.6k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.2 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 22 months ago by 68k • written 22 months ago by • 0
1
vote
4
replies
1.1k
views
How to annotate mir4.1 arrays?
AffymetrixChip miRNA oligo
24 months ago • updated 21 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
1
reply
885
views
Can't make a boxplot or hist with oligo
oligo
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
0
votes
1
reply
782
views
I need the pd.cytoscanhd.array.
oligo
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
5
replies
1.6k
views
oligo rma() background normalization crash in basicRMA()
basicRMA crash rma oligo
2.2 years ago Steffen Moeller ▴ 90
1
vote
6
replies
2.0k
views
How to annotate Data with oligo and Affymetrix HuGene-2_0-st package?
oligo
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
2
votes
2
replies
1.2k
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
2.9 years ago Yang Shi ▴ 10
2
votes
5
replies
1.5k
views
Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1 oligo AffymetrixChip
2.9 years ago Yang Shi ▴ 10
2
votes
4
replies
1.6k
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219 oligo AffymetrixChip
2.9 years ago Yang Shi ▴ 10
4
votes
10
replies
2.6k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
3.0 years ago • updated 2.9 years ago Yang Shi ▴ 10
3
votes
4
replies
2.5k
views
Quantile Normalization after rma or not?
limma Microarray oligo
3.0 years ago • updated 2.9 years ago Yang Shi ▴ 10
2
votes
2
replies
1.2k
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
3.0 years ago Yang Shi ▴ 10
1
vote
2
replies
1.5k
views
oligo package blas error
rma openblas blas oligo
3.6 years ago ch_el ▴ 10
0
votes
1
reply
874
views
Clariom-D array - subsetting probes to known genes prior to normalization
oligo
updated 3.7 years ago by 68k • written 3.7 years ago by ▴ 10
1
vote
16
replies
5.0k
views
cant read celfiles using oligo package
oligo
3.7 years ago scipio04 • 0
2
votes
8
replies
1.6k
views
pdInfoBuilder created problematic package for Affymetrix chip tiling array
oligoClasses oligo pdInfoBuilder
3.8 years ago • updated 3.7 years ago efoss ▴ 10
2
votes
1
reply
3.6k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO oligo
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
2
votes
5
replies
2.2k
views
Summarize Microarray data on a transcript level
pd.clariom.d.human oligo clariomdhumanprobeset.db
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
5
votes
8
replies
3.2k
views
how to annotate arrays
affy annotation microarray oligo
updated 4.4 years ago by 68k • written 9.7 years ago by • 0
0
votes
2
replies
1.8k
views
Annotation clariom D microarray
clariomdhumantranscriptcluster.db oligo
4.5 years ago Luca • 0
0
votes
2
replies
1.6k
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
4.5 years ago Luca • 0
0
votes
1
reply
1.1k
views
Plot legend with oligo::hist()
oligo
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 10
1
vote
1
reply
1.0k
views
Is it possible to run arrayQualitymetrics or some similar package on a HTAFeatureSet?
arrayQualityMetrics oligo
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Annotation package generation for HTA-2_0 by pdInfoBuilder fails
microarray pdInfoBuilder oligo
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
0
votes
1
reply
1.3k
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
3
votes
4
replies
3.9k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 5.2 years ago by • 0 • written 6.3 years ago by • 0
0
votes
1
reply
788
views
normalized multiple microarrays with different design files oligo
microarray oligo
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
0
votes
1
reply
1.7k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 5.4 years ago by • 0 • written 6.3 years ago by ★ 4.1k
0
votes
2
replies
1.4k
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy rma frma oligo
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
3
replies
2.1k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 20
3
votes
2
replies
2.9k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 20
0
votes
1
reply
2.5k
views
R: oligo packages install error
oligo packages error
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
1
vote
2
replies
1.8k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 5.8 years ago by 68k • written 5.8 years ago by ★ 4.1k
2
votes
4
replies
1.9k
views
rma summarization error when normalizing using oligo and brainarray cdf
oligo brainarray mbni
5.9 years ago Moosa • 0
0
votes
3
replies
1.4k
views
Brainarray CDF with oligopackage
Brainarray CDF oligo
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 50
1
vote
5
replies
1.6k
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 840
0
votes
0
replies
1.0k
views
run OLIGO package encounters errors:
oligo
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
votes
11
replies
4.2k
views
SNP6 data to VCF
SNP oligo ASSIGN SNP oligo ASSIGN
updated 6.6 years ago by • 0 • written 13.2 years ago by 21k
0
votes
5
replies
2.3k
views
Annotating Expression Set for GSVA w/ Brainarray Human Gene 1.1 ST Array CDF
bioconductor brainarray genefilter oligo
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
votes
1
reply
1.4k
views
Error: 'unknown input format' while trying http://bioconductor.org/packages/3.7/bioc
error oligo affy
7.0 years ago kritikamish99 ▴ 10
0
votes
8
replies
4.6k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 7.1 years ago by • 0 • written 11.2 years ago by ▴ 300
0
votes
1
reply
1.3k
views
Making microarray probeset presence/absence calls
oligo
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 80
0
votes
2
replies
1.6k
views
error message from oligo package
oligo
updated 3.7 years ago by • 0 • written 7.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
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