Showing : oligo • reset
0
votes
4
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361
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
4 weeks ago • updated 25 days ago Efra • 0
0
votes
2
replies
356
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
0
votes
3
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1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.1 years ago by • 0
0
votes
5
replies
2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 10.3 years ago by ★ 13k
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
2
votes
1
reply
654
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
645
views
How to annotate mir4.1 arrays?
AffymetrixChip miRNA oligo
11 months ago • updated 8 months ago richardallenfriedmanbrooklyn ▴ 20
0
votes
1
reply
579
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
458
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 • updated 13 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
851
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
1.0k
views
Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1 oligo AffymetrixChip
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
790
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
990
views
oligo package blas error
rma openblas blas oligo
2.6 years ago ch_el ▴ 10
0
votes
1
reply
624
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
1.1k
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
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
5
votes
8
replies
2.5k
views
how to annotate arrays
affy annotation microarray oligo
updated 3.4 years ago by 65k • written 8.7 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
825
views
Plot legend with oligo::hist()
oligo
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
1
vote
1
reply
768
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
909
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
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
572
views
normalized multiple microarrays with different design files oligo
microarray oligo
updated 4.2 years ago by 65k • written 4.2 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
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
2.2k
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
985
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
788
views
run OLIGO package encounters errors:
oligo
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
0
votes
11
replies
3.5k
views
SNP6 data to VCF
SNP oligo ASSIGN SNP oligo ASSIGN
updated 5.6 years ago by • 0 • written 12.2 years ago by 21k
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
8
replies
4.0k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 6.1 years ago by • 0 • written 10.2 years ago by ▴ 300
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
50 results • Page 1 of 1
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Comment: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia) by christianhilton64 • 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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