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Oligo
•
reset
1
vote
8
replies
8.7k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo
limma
bioconductor
affymetrix microarrays
8.8 years ago
Claudia
▴ 10
0
votes
17
replies
8.2k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation
Normalization
GO
PROcess
oligo
Annotation
Normalization
GO
PROcess
oligo
updated 11.1 years ago by
James W. MacDonald
65k • written 11.1 years ago by
Kamila Naxerova
▴ 100
0
votes
4
replies
6.5k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo
annotate
6.4 years ago
llkxiaolan
▴ 10
0
votes
4
replies
6.4k
views
Problem "Error: is.character(filenames) is not TRUE" in read.xysfiles (Oligo package)
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 10.0 years ago by
James W. MacDonald
65k • written 10.0 years ago by
Tommaso Raffaello
▴ 60
7
votes
4
replies
5.7k
views
Gene symbols on MA-plot
limma
plot.MA
volcanoplot
oligo
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
Gabriel Nathan Kaufman, Mr
▴ 60
7
votes
6
replies
5.5k
views
How to use brainarray custom cdf with oligo package?
oligo
customcdf
HTA
frma
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
sanj
▴ 20
2
votes
5
replies
5.4k
views
Oligo package RMA() function giving error
oligo
rma
updated 8.7 years ago by
Benilton Carvalho
★ 4.3k • written 8.7 years ago by
Jo
▴ 30
0
votes
5
replies
5.4k
views
How to do Affy ST array analysis
Annotation
Normalization
hgu133a
probe
affy
oligo
Annotation
Normalization
hgu133a
probe
updated 8.9 years ago by
benhrif.oussama
• 0 • written 10.0 years ago by
Guest User
★ 13k
0
votes
12
replies
5.2k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray
GO
oligo
AnnotationForge
Microarray
GO
oligo
AnnotationForge
11.2 years ago
James W. MacDonald
65k
1
vote
10
replies
5.2k
views
How to use brainarray custom cdf with any bioconductor package?
affy
oligo
customcdf
9.4 years ago • updated 9.0 years ago
rishi.dasroy
▴ 20
3
votes
5
replies
5.0k
views
getBM returns shorter vectors than values
annotate
biomaRt
oligo
annotate
biomaRt
oligo
updated 10.6 years ago by
Steffen Durinck
▴ 540 • written 10.6 years ago by
Lescai, Francesco
▴ 380
1
vote
4
replies
4.3k
views
Transcript to gene in clariom d human affymetrix data
annotation
clariomdhumantranscriptcluster.db
oligo
7.1 years ago
yahia.adnani
• 0
0
votes
4
replies
4.3k
views
An error in oligo: All the CEL files must be of the same type??
BiocViews
Annotation
Organism
biocViews
oligo
BiocViews
BiocViews
Annotation
Organism
updated 12.9 years ago by
Benilton Carvalho
★ 4.3k • written 12.9 years ago by
Setsuko Sahara
▴ 20
0
votes
7
replies
4.3k
views
How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip
annotation
oligo
updated 6.4 years ago by
Guido Hooiveld
★ 3.9k • written 6.4 years ago by
llkxiaolan
▴ 10
10
votes
13
replies
4.3k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R
limma
oligo
differential gene expression
affymetrix microarrays
updated 8.8 years ago by
tree-ski
• 0 • written 8.8 years ago by
dennis.oezcelik
▴ 10
3
votes
9
replies
4.2k
views
Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
microarray
normalization
oligo
updated 8.4 years ago by
burchard
• 0 • written 9.5 years ago by
tangboyun
▴ 30
1
vote
3
replies
4.1k
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
0
votes
4
replies
4.1k
views
Problem reading Cel files - Oligo Package
Annotation
oligo
Annotation
oligo
updated 10.6 years ago by
James W. MacDonald
65k • written 10.6 years ago by
Bade
▴ 310
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
6
votes
22
replies
3.9k
views
Oligo package: paCalls questions
microarray
oligo
updated 8.9 years ago by
cstrato
★ 3.9k • written 8.9 years ago by
whyuen
▴ 20
9
votes
6
replies
3.9k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray
oligo
affycoretools
pd.hugene.2.0.st
hugene20sttranscriptcluster.db
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
svlachavas
▴ 830
1
vote
11
replies
3.8k
views
oligo package requires the annotation package pd.ht.mg.430.pm - where is it?
oligo
microarray
annotation
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
peer.karmaus
• 0
0
votes
3
replies
3.7k
views
How do I choose between using affy or oligo package for preprocessing microarrays?
microarray
affymetrix microarrays
affy
oligo
updated 3.1 years ago by
James W. MacDonald
65k • written 7.2 years ago by
stevessheridan
• 0
0
votes
4
replies
3.6k
views
exprs() in Bioc 2.10
probe
affy
oligo
probe
affy
oligo
updated 12.0 years ago by
Benilton Carvalho
★ 4.3k • written 12.0 years ago by
Michael Morley
▴ 30
2
votes
14
replies
3.5k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma
oligo
annotation
updated 9.1 years ago by
alakatos
▴ 130 • written 9.3 years ago by
aminbau14
• 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
1
vote
16
replies
3.4k
views
cant read celfiles using oligo package
oligo
2.7 years ago
scipio04
• 0
0
votes
1
reply
3.3k
views
Error to import Data Affymetrix
affy
oligo
xps
affy
oligo
xps
updated 10.9 years ago by
Steve Lianoglou
★ 13k • written 10.9 years ago by
Guest User
★ 13k
6
votes
7
replies
3.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 23 months ago by
Yang Shi
▴ 10 • written 7.0 years ago by
svlachavas
▴ 830
2
votes
4
replies
3.1k
views
Error with boxplot command from oligo package with raw Affy data
oligo
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
johnlee.johnson
• 0
3
votes
4
replies
3.0k
views
pd.huex.1.0.st.v2 package doubt
oligo
exon array analysis
updated 8.9 years ago by
Marc Carlson
★ 7.2k • written 8.9 years ago by
Elena Serrano
▴ 30
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
2
replies
2.9k
views
Error with oligo: environmentIsLocked
oligo
bioconductor
genefilter
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
Claudia
▴ 10
0
votes
3
replies
2.8k
views
GWAS with Affymetrix SNP 6.0
SNP
oligo
snpMatrix
snpStats
SNP
oligo
snpMatrix
snpStats
updated 11.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.9 years ago by
David Hervás
▴ 20
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
0
votes
0
replies
2.7k
views
DE analysis pipeline with Hugene 2.0 ST arrays
hugene20
microarray
limma
limma paired analysis
oligo
8.2 years ago
hakimelakhrass
• 0
0
votes
10
replies
2.7k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray
Normalization
cdf
oligo
DTA
Microarray
Normalization
cdf
oligo
DTA
updated 14.2 years ago by
Benilton Carvalho
★ 4.3k • written 14.2 years ago by
Mikhail Pachkov
▴ 110
0
votes
1
reply
2.7k
views
Analysis of Human Gene 1.1 ST Array
Microarray
cdf
affy
PROcess
oligo
xps
Microarray
cdf
affy
PROcess
oligo
xps
updated 10.5 years ago by
James W. MacDonald
65k • written 10.5 years ago by
Jerry Cholo
▴ 190
2
votes
16
replies
2.7k
views
Possible ways of performing non-specific intensity filtering on Perfect-match only affymetrix array
oligo
DABG
non-specific filtering
primeview
9.0 years ago
svlachavas
▴ 830
0
votes
3
replies
2.7k
views
Questions about analysis of Human Gene 2.0 ST Array
oligo
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
Biologist
▴ 110
0
votes
4
replies
2.6k
views
topGO w/custom annotation
Annotation
GO
oligo
Annotation
GO
oligo
updated 15.9 years ago by
James W. MacDonald
65k • written 15.9 years ago by
Sebastien Gerega
▴ 370
3
votes
3
replies
2.6k
views
Problem using RMA Method in 'Oligo' with HTAFeatureset Objects
affymetrix microarrays
microarray
pd.hta.2.0
oligo
rma
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
jennifer.drake
• 0
0
votes
5
replies
2.6k
views
Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
Annotation
probe
annotate
annaffy
oligo
ReportingTools
Annotation
probe
annotate
annaffy
updated 9.8 years ago by
Jason Hackney
▴ 160 • written 9.9 years ago by
James W. MacDonald
65k
0
votes
15
replies
2.6k
views
PreFiltering probe in microarray analysis
Microarray
limma
oligo
Microarray
limma
oligo
updated 12.9 years ago by
wxu@msi.umn.edu
▴ 220 • written 12.9 years ago by
Stephanie PIERSON
▴ 30
0
votes
0
replies
2.6k
views
Seperate quantile normalization but common probe summary by median polish (oligo package)?
Normalization
probe
oligo
frma
frmaTools
Normalization
probe
oligo
frma
frmaTools
11.7 years ago
Schott, Johanna
▴ 20
0
votes
0
replies
2.5k
views
Importing quantile normalized .txt file to limma for differential expression
Normalization
affy
limma
oligo
xps
Normalization
affy
limma
oligo
xps
10.6 years ago
James W. MacDonald
65k
0
votes
5
replies
2.5k
views
Load CDF files for Affymetrix ST 2.0 microarrays
microarray
oligo
cdf
customcdf
updated 8.4 years ago by
Guido Hooiveld
★ 3.9k • written 8.4 years ago by
Nathaniel
▴ 20
1
vote
2
replies
2.5k
views
Warning Message-depreciated after running rma in oligo package
oligo
pd.ragene.2.0.st
9.1 years ago
Surles, Monique
▴ 50
2
votes
6
replies
2.5k
views
Questions about analysis of GeneChip Rat Gene 2.0 ST Array
microarray
affy
oligo
annotation
9.2 years ago
khosoda
• 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
50 results • Page
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Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
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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