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Views
Votes
Showing :
oligo
•
reset
0
votes
1
reply
223
views
Custom CDF creation for HTA 2.0 array using GTF annotation
oligo
oligoClasses
pdInfoBuilder
affycoretools
affyio
14 days ago • updated 13 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
850
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
13 months ago
Efra
• 0
0
votes
2
replies
936
views
Error Oligo package asking for pd.2.0 package annotation
oligo
updated 16 months ago by
Guido Hooiveld
★ 4.1k • written 16 months ago by
alantb_cederj
• 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
tanya
• 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
Guest User
★ 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
chandlerjd58
▴ 10
2
votes
1
reply
1.5k
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData
DataImport
oligo
RNASeqData
convert
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
rodj5201
• 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
882
views
Can't make a boxplot or hist with oligo
oligo
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
i.am.filippov
• 0
0
votes
1
reply
777
views
I need the pd.cytoscanhd.array.
oligo
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
bakaka0518
• 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
James W. MacDonald
68k • written 2.6 years ago by
sebast1an
• 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
2.9 years ago
Yang Shi
▴ 10
3
votes
4
replies
2.4k
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
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
2.9 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
873
views
Clariom-D array - subsetting probes to known genes prior to normalization
oligo
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
Lauro Sumoy
▴ 10
1
vote
16
replies
4.9k
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
James W. MacDonald
68k • written 4.1 years ago by
Gero
• 0
2
votes
5
replies
2.2k
views
Summarize Microarray data on a transcript level
pd.clariom.d.human
oligo
clariomdhumanprobeset.db
updated 4.3 years ago by
James W. MacDonald
68k • written 4.3 years ago by
mailtoshivam13
• 0
5
votes
8
replies
3.2k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 4.4 years ago by
James W. MacDonald
68k • written 9.7 years ago by
ben_cossins
• 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
James W. MacDonald
68k • written 4.6 years ago by
Jeni
▴ 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
James W. MacDonald
68k • written 4.6 years ago by
Jeni
▴ 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
James W. MacDonald
68k • written 4.8 years ago by
Marton Papp
• 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
James W. MacDonald
68k • written 5.0 years ago by
lsbew
• 0
3
votes
4
replies
3.9k
views
lm.fit incompatible dimensions
oligo
arrayexpress
limma
updated 5.2 years ago by
Anna Woods
• 0 • written 6.3 years ago by
maxininfa
• 0
0
votes
1
reply
787
views
normalized multiple microarrays with different design files oligo
microarray
oligo
updated 5.3 years ago by
James W. MacDonald
68k • written 5.3 years ago by
benjamin-gansemer
• 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
Rise
• 0 • written 6.3 years ago by
Guido Hooiveld
★ 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 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
chziy429
• 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
James W. MacDonald
68k • written 5.5 years ago by
salamandra
▴ 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
James W. MacDonald
68k • written 5.5 years ago by
salamandra
▴ 20
0
votes
1
reply
2.5k
views
R: oligo packages install error
oligo
packages
error
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
get3232
• 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
James W. MacDonald
68k • written 5.8 years ago by
Guido Hooiveld
★ 4.1k
2
votes
4
replies
1.9k
views
rma summarization error when normalizing using oligo and brainarray cdf
oligo
brainarray
mbni
5.8 years ago
Moosa
• 0
0
votes
3
replies
1.4k
views
Brainarray CDF with oligopackage
Brainarray CDF
oligo
updated 6.0 years ago by
James W. MacDonald
68k • written 6.0 years ago by
pbachali
▴ 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
James W. MacDonald
68k • written 6.1 years ago by
svlachavas
▴ 840
0
votes
0
replies
1.0k
views
run OLIGO package encounters errors:
oligo
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
83310199
• 0
0
votes
11
replies
4.2k
views
SNP6 data to VCF
SNP
oligo
ASSIGN
SNP
oligo
ASSIGN
updated 6.6 years ago by
giulio.genovese
• 0 • written 13.2 years ago by
Sean Davis
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
James W. MacDonald
68k • written 6.9 years ago by
kdyson
• 0
0
votes
1
reply
1.4k
views
Error: 'unknown input format' while trying http://bioconductor.org/packages/3.7/bioc
error
oligo
affy
6.9 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
joseph.a.white1
• 0 • written 11.2 years ago by
nooshin
▴ 300
0
votes
1
reply
1.3k
views
Making microarray probeset presence/absence calls
oligo
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
mat149
▴ 80
0
votes
2
replies
1.6k
views
error message from oligo package
oligo
updated 3.7 years ago by
Jesús
• 0 • written 7.3 years ago by
chchen
• 0
50 results • Page
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Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2
by
cold.wolverine.arku
• 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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