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Showing :
Oligo
•
reset
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
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
1
vote
16
replies
3.4k
views
cant read celfiles using oligo package
oligo
2.7 years ago
scipio04
• 0
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
7
votes
16
replies
2.4k
views
Can "Glue Grant" arrays be processed with pd.hta.2.0?
pd.hta.2.0
ggh3
oligo
glue grant
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
Robert Castelo
★ 3.2k
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
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
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
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
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
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
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
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
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
4
votes
10
replies
2.3k
views
Limma/oligo always crashing
limma
microarray
pd.hugene.2.0.st
hugene20
oligo
8.2 years ago
hakimelakhrass
• 0
0
votes
10
replies
1.8k
views
One-color spotted microarrays analysis
Microarray
Normalization
oligo
Microarray
Normalization
oligo
updated 14.9 years ago by
Wolfgang Huber
★ 13k • written 14.9 years ago by
Pier-Luc Poulin
▴ 30
3
votes
10
replies
1.9k
views
Still need help identifying a good workflow for finding DEG in hugene 2.0 st
microarray
hugene20
limma
oligo
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
hakimelakhrass
• 0
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
0
votes
9
replies
2.4k
views
using frma and brainarray cdf on exon arrays
cdf
affy
PROcess
oligo
xps
frma
cdf
affy
PROcess
oligo
xps
frma
updated 10.3 years ago by
Stephen Piccolo
▴ 590 • written 10.3 years ago by
Ty Thomson
▴ 100
0
votes
9
replies
1.4k
views
pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R
oligo
oligo
updated 14.5 years ago by
Benilton Carvalho
★ 4.3k • written 14.5 years ago by
Adeline Simon
▴ 50
0
votes
9
replies
1.6k
views
RE: Advice on print-tip normalization
Cancer
probe
marray
oligo
Cancer
probe
marray
oligo
updated 19.6 years ago by
Gene Cutler
▴ 50 • written 19.6 years ago by
Mark Reimers
▴ 70
0
votes
9
replies
1.3k
views
Masking single Oligos in mas5
oligo
oligo
updated 18.4 years ago by
Jenny Drnevich
★ 2.2k • written 18.4 years ago by
Benjamin Otto
▴ 830
0
votes
9
replies
2.2k
views
RNA degradation plot with oligo package GeneFeatureSet objects
affy
oligo
affy
oligo
updated 10.7 years ago by
James W. MacDonald
65k • written 10.7 years ago by
heyi xiao
▴ 360
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
0
votes
8
replies
1.6k
views
oligo on R 2.4.1?
GO
Survival
annotate
genefilter
affy
affydata
matchprobes
affyQCReport
affyio
oligo
GO
updated 17.2 years ago by
Seth Falcon
★ 7.4k • written 17.2 years ago by
Jenny Drnevich
★ 2.2k
0
votes
8
replies
2.1k
views
vsn preprocess with oligo package
vsn
oligo
oligoClasses
vsn
oligo
oligoClasses
updated 11.3 years ago by
James W. MacDonald
65k • written 11.3 years ago by
José LÓPEZ
▴ 110
0
votes
8
replies
2.0k
views
pdInfoBuilder: invalid class object ("ScalarCharacter")
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 14.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 14.0 years ago by
Guido Hooiveld
★ 3.9k
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
8
replies
2.2k
views
Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
affy
aroma.affymetrix
exon array
xps
oligo
6.8 years ago
Gordon Smyth
50k
0
votes
8
replies
2.3k
views
HTA 2.0 ST array annotation
hta20sttranscriptcluster.db
oligo
updated 8.2 years ago by
James W. MacDonald
65k • written 8.2 years ago by
sylvia
▴ 10
0
votes
8
replies
1.5k
views
crlmm warning
oligo
crlmm
oligo
crlmm
updated 17.1 years ago by
Benilton Carvalho
★ 4.3k • written 17.1 years ago by
Morten Mattingsdal
▴ 190
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
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
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
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
3
votes
7
replies
1.7k
views
Oligo: cannot fit robust Probe Level linear Models / fitPLM when using a custom CDF
oligo
pdinfobuilder
pd.mogene.1.1.st
customcdf
updated 7.5 years ago by
James W. MacDonald
65k • written 8.1 years ago by
Guido Hooiveld
★ 3.9k
0
votes
7
replies
1.5k
views
presence/absence call using oligo array?
Microarray
oligo
Microarray
oligo
18.3 years ago
xpeng
▴ 60
0
votes
6
replies
1.8k
views
Bioc packages not working with R2.15.2?
Cancer
oligo
Cancer
oligo
updated 11.4 years ago by
Benilton Carvalho
★ 4.3k • written 11.4 years ago by
Yongde Bao
▴ 170
0
votes
6
replies
1.5k
views
QC Affy 6.0 SNP arrays with crlmm or Oligo?
Normalization
oligo
crlmm
Normalization
oligo
crlmm
updated 14.1 years ago by
Benilton Carvalho
★ 4.3k • written 14.1 years ago by
jeremy wilson
▴ 150
0
votes
6
replies
1.6k
views
Normalization between arrays for common reference, time course and direct two color designs
Normalization
limma
oligo
Normalization
limma
oligo
17.4 years ago
Jenny Drnevich
★ 2.2k
0
votes
6
replies
1.6k
views
PdInfoBuilder for nimblegen array
Annotation
Organism
oligo
pdInfoBuilder
Annotation
Organism
oligo
pdInfoBuilder
updated 14.2 years ago by
Benilton Carvalho
★ 4.3k • written 14.2 years ago by
Alex Rodriguez
▴ 40
1
vote
6
replies
1.7k
views
oligo: crash/segfault when fitting probelevel model
oligo
openblas
preprocessCore
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
Guido Hooiveld
★ 3.9k
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
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
2
votes
6
replies
1.7k
views
Help: obtain Entrez ID's from limma top table with Affymetrix microarray (pd.zebgene.1.1.st)
affmetrix
microarray
limma
oligo
updated 7.5 years ago by
James W. MacDonald
65k • written 7.5 years ago by
mat149
▴ 70
0
votes
6
replies
1.4k
views
Human Gene ST using oligo package
Annotation
oligo
Annotation
oligo
updated 13.9 years ago by
Benilton Carvalho
★ 4.3k • written 13.9 years ago by
Javier Pérez Florido
▴ 840
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
1
vote
6
replies
1.2k
views
Intronic sequences are the majority of the top differentially expressed genes
limma
microarray
normalization
oligo
differential gene expression
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
ben_cossins
• 0
5
votes
6
replies
2.2k
views
Error installing pd.huex.1.0.st.v2: database disk image is malformed
pd.huex.1.0.st.v2
oligo
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
Guido Hooiveld
★ 3.9k
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
50 results • Page
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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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