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Showing :
Oligo
•
reset
0
votes
4
replies
367
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
5 weeks ago • updated 29 days ago
Efra
• 0
0
votes
2
replies
361
views
Error Oligo package asking for pd.2.0 package annotation
oligo
updated 4 months ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
alantb_cederj
• 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
tanya
• 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
Guest User
★ 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
chandlerjd58
▴ 10
2
votes
1
reply
662
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
James W. MacDonald
65k • written 9 months ago by
rodj5201
• 0
1
vote
4
replies
655
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
James W. MacDonald
65k • written 12 months ago by
i.am.filippov
• 0
0
votes
1
reply
461
views
I need the pd.cytoscanhd.array.
oligo
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
bakaka0518
• 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
James W. MacDonald
65k • written 19 months ago by
sebast1an
• 0
2
votes
2
replies
856
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
627
views
Clariom-D array - subsetting probes to known genes prior to normalization
oligo
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
Lauro Sumoy
▴ 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
James W. MacDonald
65k • written 3.1 years ago by
Gero
• 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
James W. MacDonald
65k • written 3.3 years ago by
mailtoshivam13
• 0
5
votes
8
replies
2.5k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 3.4 years ago by
James W. MacDonald
65k • written 8.7 years ago by
ben_cossins
• 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
James W. MacDonald
65k • written 3.6 years ago by
Jeni
▴ 10
1
vote
1
reply
773
views
Is it possible to run arrayQualitymetrics or some similar package on a HTAFeatureSet?
arrayQualityMetrics
oligo
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
Jeni
▴ 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
James W. MacDonald
65k • written 3.8 years ago by
Marton Papp
• 0
0
votes
1
reply
916
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy
oligo
Clariom S Mouse
microarray
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
lsbew
• 0
3
votes
4
replies
2.9k
views
lm.fit incompatible dimensions
oligo
arrayexpress
limma
updated 4.2 years ago by
Anna Woods
• 0 • written 5.3 years ago by
maxininfa
• 0
0
votes
1
reply
577
views
normalized multiple microarrays with different design files oligo
microarray
oligo
updated 4.3 years ago by
James W. MacDonald
65k • written 4.3 years ago by
benjamin-gansemer
• 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
Rise
• 0 • written 5.3 years ago by
Guido Hooiveld
★ 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
James W. MacDonald
65k • written 4.4 years ago by
chziy429
• 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
James W. MacDonald
65k • written 4.5 years ago by
salamandra
▴ 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
James W. MacDonald
65k • written 4.5 years ago by
salamandra
▴ 20
0
votes
1
reply
1.7k
views
R: oligo packages install error
oligo
packages
error
updated 4.8 years ago by
Martin Morgan
25k • written 4.8 years ago by
get3232
• 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
James W. MacDonald
65k • written 4.8 years ago by
Guido Hooiveld
★ 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
987
views
Brainarray CDF with oligopackage
Brainarray CDF
oligo
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
pbachali
▴ 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
James W. MacDonald
65k • written 5.1 years ago by
svlachavas
▴ 830
0
votes
0
replies
795
views
run OLIGO package encounters errors:
oligo
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
83310199
• 0
0
votes
11
replies
3.5k
views
SNP6 data to VCF
SNP
oligo
ASSIGN
SNP
oligo
ASSIGN
updated 5.6 years ago by
giulio.genovese
• 0 • written 12.2 years ago by
Sean Davis
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
James W. MacDonald
65k • written 5.9 years ago by
kdyson
• 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
joseph.a.white1
• 0 • written 10.2 years ago by
nooshin
▴ 300
0
votes
1
reply
1.0k
views
Making microarray probeset presence/absence calls
oligo
updated 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
mat149
▴ 70
0
votes
2
replies
1.3k
views
error message from oligo package
oligo
updated 2.7 years ago by
Jesús
• 0 • written 6.3 years ago by
chchen
• 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
SamGG
▴ 350 • written 6.3 years ago by
Biologist
▴ 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
Recent ...
Replies
Comment: Different Shrunk Log2FC according with reference
by
Michael Love
41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
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