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Showing :
Oligo
•
reset
6
votes
22
replies
2.5k
views
Oligo package: paCalls questions
microarray
oligo
updated 7.0 years ago by
cstrato
★ 3.9k • written 7.0 years ago by
whyuen
▴ 20
0
votes
17
replies
6.8k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation
Normalization
GO
PROcess
oligo
Annotation
Normalization
GO
PROcess
oligo
updated 9.2 years ago by
James W. MacDonald
59k • written 9.2 years ago by
Kamila Naxerova
▴ 100
7
votes
16
replies
1.6k
views
Can "Glue Grant" arrays be processed with pd.hta.2.0?
pd.hta.2.0
ggh3
oligo
glue grant
updated 6.4 years ago by
James W. MacDonald
59k • written 6.4 years ago by
Robert Castelo
★ 2.9k
1
vote
16
replies
861
views
cant read celfiles using oligo package
oligo
9 months ago
scipio04
• 0
2
votes
16
replies
1.9k
views
Possible ways of performing non-specific intensity filtering on Perfect-match only affymetrix array
oligo
DABG
non-specific filtering
primeview
7.1 years ago
svlachavas
▴ 780
0
votes
15
replies
1.8k
views
PreFiltering probe in microarray analysis
Microarray
limma
oligo
Microarray
limma
oligo
updated 11.0 years ago by
wxu@msi.umn.edu
▴ 220 • written 11.0 years ago by
Stephanie PIERSON
▴ 30
2
votes
14
replies
2.7k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma
oligo
annotation
updated 7.2 years ago by
alakatos
▴ 120 • written 7.4 years ago by
aminbau14
• 0
10
votes
13
replies
3.2k
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 6.9 years ago by
tree-ski
• 0 • written 6.9 years ago by
dennis.oezcelik
▴ 10
0
votes
12
replies
3.1k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray
GO
oligo
AnnotationForge
Microarray
GO
oligo
AnnotationForge
9.3 years ago
James W. MacDonald
59k
1
vote
11
replies
2.3k
views
oligo package requires the annotation package pd.ht.mg.430.pm - where is it?
oligo
microarray
annotation
updated 6.7 years ago by
James W. MacDonald
59k • written 6.7 years ago by
peer.karmaus
• 0
0
votes
11
replies
2.4k
views
SNP6 data to VCF
SNP
oligo
ASSIGN
SNP
oligo
ASSIGN
updated 3.7 years ago by
giulio.genovese
• 0 • written 10.3 years ago by
Sean Davis
21k
4
votes
10
replies
221
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
5 days ago • updated 4 days ago
Yang Shi
• 0
0
votes
10
replies
1.8k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray
Normalization
cdf
oligo
DTA
Microarray
Normalization
cdf
oligo
DTA
updated 12.2 years ago by
Benilton Carvalho
★ 4.3k • written 12.2 years ago by
Mikhail Pachkov
▴ 110
1
vote
10
replies
4.4k
views
How to use brainarray custom cdf with any bioconductor package?
affy
oligo
customcdf
7.5 years ago • updated 7.1 years ago
rishi.dasroy
▴ 20
4
votes
10
replies
1.6k
views
Limma/oligo always crashing
limma
microarray
pd.hugene.2.0.st
hugene20
oligo
6.3 years ago
hakimelakhrass
• 0
3
votes
10
replies
1.2k
views
Still need help identifying a good workflow for finding DEG in hugene 2.0 st
microarray
hugene20
limma
oligo
updated 6.3 years ago by
Aaron Lun
★ 27k • written 6.3 years ago by
hakimelakhrass
• 0
0
votes
10
replies
1.2k
views
One-color spotted microarrays analysis
Microarray
Normalization
oligo
Microarray
Normalization
oligo
updated 13.0 years ago by
Wolfgang Huber
13k • written 13.0 years ago by
Pier-Luc Poulin
▴ 30
3
votes
9
replies
3.4k
views
Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
microarray
normalization
oligo
updated 6.5 years ago by
burchard
• 0 • written 7.6 years ago by
tangboyun
▴ 30
0
votes
9
replies
912
views
RE: Advice on print-tip normalization
Cancer
probe
marray
oligo
Cancer
probe
marray
oligo
updated 17.7 years ago by
Gene Cutler
▴ 50 • written 17.7 years ago by
Mark Reimers
▴ 70
0
votes
9
replies
964
views
pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R
oligo
oligo
updated 12.6 years ago by
Benilton Carvalho
★ 4.3k • written 12.6 years ago by
Adeline Simon
▴ 50
0
votes
9
replies
1.6k
views
using frma and brainarray cdf on exon arrays
cdf
affy
PROcess
oligo
xps
frma
cdf
affy
PROcess
oligo
xps
frma
updated 8.4 years ago by
Stephen Piccolo
▴ 580 • written 8.4 years ago by
Ty Thomson
▴ 100
0
votes
9
replies
756
views
Masking single Oligos in mas5
oligo
oligo
updated 16.5 years ago by
Jenny Drnevich
★ 2.2k • written 16.5 years ago by
Benjamin Otto
▴ 830
0
votes
9
replies
1.6k
views
RNA degradation plot with oligo package GeneFeatureSet objects
affy
oligo
affy
oligo
updated 8.8 years ago by
James W. MacDonald
59k • written 8.8 years ago by
heyi xiao
▴ 360
2
votes
8
replies
411
views
pdInfoBuilder created problematic package for Affymetrix chip tiling array
oligoClasses
oligo
pdInfoBuilder
10 months ago • updated 9 months ago
efoss
▴ 10
5
votes
8
replies
1.6k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 17 months ago by
James W. MacDonald
59k • written 6.8 years ago by
ben_cossins
• 0
0
votes
8
replies
1.0k
views
oligo on R 2.4.1?
GO
Survival
annotate
genefilter
affy
affydata
matchprobes
affyQCReport
affyio
oligo
GO
updated 15.3 years ago by
Seth Falcon
★ 7.4k • written 15.3 years ago by
Jenny Drnevich
★ 2.2k
0
votes
8
replies
1.4k
views
vsn preprocess with oligo package
vsn
oligo
oligoClasses
vsn
oligo
oligoClasses
updated 9.4 years ago by
James W. MacDonald
59k • written 9.4 years ago by
José LÓPEZ
▴ 110
0
votes
8
replies
1.9k
views
HTA 2.0 ST array annotation
hta20sttranscriptcluster.db
oligo
updated 6.3 years ago by
James W. MacDonald
59k • written 6.3 years ago by
sylvia
▴ 10
0
votes
8
replies
2.7k
views
error ReadAffy
Arabidopsis thaliana
cdf
affy
gcrma
PROcess
oligo
xps
Arabidopsis thaliana
cdf
affy
xps
updated 4.2 years ago by
joseph.a.white1
• 0 • written 8.3 years ago by
nooshin
▴ 300
6
votes
8
replies
1.4k
views
Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
affy
aroma.affymetrix
exon array
xps
oligo
4.9 years ago
Gordon Smyth
45k
0
votes
8
replies
1.3k
views
pdInfoBuilder: invalid class object ("ScalarCharacter")
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 12.1 years ago by
Vincent J. Carey, Jr.
6.6k • written 12.1 years ago by
Guido Hooiveld
★ 3.2k
0
votes
8
replies
1.1k
views
crlmm warning
oligo
crlmm
oligo
crlmm
updated 15.2 years ago by
Benilton Carvalho
★ 4.3k • written 15.2 years ago by
Morten Mattingsdal
▴ 190
1
vote
8
replies
6.4k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo
limma
bioconductor
affymetrix microarrays
6.8 years ago
Claudia
▴ 10
0
votes
7
replies
2.7k
views
How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip
annotation
oligo
updated 4.5 years ago by
Guido Hooiveld
★ 3.2k • written 4.5 years ago by
llkxiaolan
• 0
6
votes
7
replies
2.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 8 days ago by
Yang Shi
• 0 • written 5.1 years ago by
svlachavas
▴ 780
0
votes
7
replies
834
views
presence/absence call using oligo array?
Microarray
oligo
Microarray
oligo
16.4 years ago
xpeng
▴ 60
3
votes
7
replies
1.2k
views
Oligo: cannot fit robust Probe Level linear Models / fitPLM when using a custom CDF
oligo
pdinfobuilder
pd.mogene.1.1.st
customcdf
updated 5.6 years ago by
James W. MacDonald
59k • written 6.2 years ago by
Guido Hooiveld
★ 3.2k
0
votes
6
replies
1.4k
views
Bioc packages not working with R2.15.2?
Cancer
oligo
Cancer
oligo
updated 9.5 years ago by
Benilton Carvalho
★ 4.3k • written 9.5 years ago by
Yongde Bao
▴ 170
0
votes
6
replies
1.1k
views
QC Affy 6.0 SNP arrays with crlmm or Oligo?
Normalization
oligo
crlmm
Normalization
oligo
crlmm
updated 12.2 years ago by
Benilton Carvalho
★ 4.3k • written 12.2 years ago by
jeremy wilson
▴ 150
0
votes
6
replies
939
views
Normalization between arrays for common reference, time course and direct two color designs
Normalization
limma
oligo
Normalization
limma
oligo
15.5 years ago
Jenny Drnevich
★ 2.2k
0
votes
6
replies
1.1k
views
PdInfoBuilder for nimblegen array
Annotation
Organism
oligo
pdInfoBuilder
Annotation
Organism
oligo
pdInfoBuilder
updated 12.3 years ago by
Benilton Carvalho
★ 4.3k • written 12.3 years ago by
Alex Rodriguez
▴ 40
1
vote
6
replies
1.1k
views
oligo: crash/segfault when fitting probelevel model
oligo
openblas
preprocessCore
updated 4.7 years ago by
James W. MacDonald
59k • written 4.7 years ago by
Guido Hooiveld
★ 3.2k
2
votes
6
replies
2.0k
views
Questions about analysis of GeneChip Rat Gene 2.0 ST Array
microarray
affy
oligo
annotation
7.3 years ago
khosoda
• 0
9
votes
6
replies
3.1k
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 5.3 years ago by
James W. MacDonald
59k • written 5.3 years ago by
svlachavas
▴ 780
2
votes
6
replies
1.1k
views
Help: obtain Entrez ID's from limma top table with Affymetrix microarray (pd.zebgene.1.1.st)
affmetrix
microarray
limma
oligo
updated 5.6 years ago by
James W. MacDonald
59k • written 5.6 years ago by
mat149
▴ 60
0
votes
6
replies
973
views
Human Gene ST using oligo package
Annotation
oligo
Annotation
oligo
updated 12.0 years ago by
Benilton Carvalho
★ 4.3k • written 12.0 years ago by
Javier Pérez Florido
▴ 840
1
vote
6
replies
881
views
Intronic sequences are the majority of the top differentially expressed genes
limma
microarray
normalization
oligo
differential gene expression
updated 6.7 years ago by
James W. MacDonald
59k • written 6.7 years ago by
ben_cossins
• 0
7
votes
6
replies
4.6k
views
How to use brainarray custom cdf with oligo package?
oligo
customcdf
HTA
frma
updated 6.7 years ago by
James W. MacDonald
59k • written 6.7 years ago by
sanj
▴ 20
5
votes
6
replies
1.4k
views
Error installing pd.huex.1.0.st.v2: database disk image is malformed
pd.huex.1.0.st.v2
oligo
updated 4.8 years ago by
James W. MacDonald
59k • written 4.8 years ago by
Guido Hooiveld
★ 3.2k
0
votes
5
replies
870
views
Development of GCRMA-like methods
gcrma
oligo
gcrma
oligo
18.3 years ago
Matthew Hannah
▴ 940
50 results • Page
1 of 1
Recent ...
Replies
Comment: CPM after RUVseq
by
James W. MacDonald
59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq
by
Jess
• 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error
by
Laurent Gatto
1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue
by
shepherl
3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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