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Affy
•
reset
0
votes
0
replies
2.6k
views
MAplot: Binning grid too coarse for current (small) bandwidth
affy
affymetrix
affymetrics
affymetrixchip
10.7 years ago
neverstop
• 0
1
vote
2
replies
2.1k
views
array quality control, affy probes, contracts setting in limma, result interpretation and weights
limma
affy
probe
qualitycontrol
design and contrast matrix
updated 10.8 years ago by
Gordon Smyth
53k • written 10.8 years ago by
alakatos
▴ 130
1
vote
3
replies
8.9k
views
Annotating limma Results with Gene Names for Affy Microarrays
limma
annotation
pd.mogene.2.0.st
mogene20sttranscriptcluster.db
affy
updated 10.8 years ago by
Gordon Smyth
53k • written 10.8 years ago by
alakatos
▴ 130
1
vote
2
replies
3.0k
views
Use junction probesets (JUC) to detect alternative splicing on Affymetrix human HTA 2.0 arrays?
microarray
affy
hta
2.0
junction
10.8 years ago
rbao.cri
• 0
0
votes
0
replies
2.1k
views
Limma design matrix for time course experiment
affy
limma
15.5 years ago • updated 10.8 years ago
Gordon Smyth
53k
0
votes
1
reply
2.1k
views
Limma design matrix for time course experiment
affy
limma
affy
limma
updated 10.8 years ago by
Gordon Smyth
53k • written 15.5 years ago by
Suresh, Uthra
▴ 10
2
votes
2
replies
1.7k
views
problem with custom cdf
microarray
affy
hgu133plus2
annotation
cdf
updated 10.8 years ago by
James W. MacDonald
68k • written 10.8 years ago by
tadoktor
• 0
0
votes
1
reply
1.2k
views
using library pd.hg.u95av2
affy
databases
10.9 years ago
Pau Marc Muñoz Torres
▴ 20
0
votes
1
reply
901
views
Determining and separating Affy Chips from GEOquery?
geoquery
affy
updated 10.9 years ago by
James W. MacDonald
68k • written 10.9 years ago by
PyPer
▴ 20
2
votes
2
replies
2.8k
views
Subsetting ESet object based on featuredata
affy
updated 10.9 years ago by
James W. MacDonald
68k • written 10.9 years ago by
kaushal Raj Chaudhary
▴ 10
1
vote
4
replies
2.0k
views
Trouble with gcrma, Segfault on background correction
gcrma
affy
updated 11.0 years ago by
James W. MacDonald
68k • written 11.0 years ago by
tangboyun
▴ 30
0
votes
0
replies
1.8k
views
Any R Package To Detect Copy Neutral LOH for SNP 6.0 Array Data
microarray
affy
snp
11.0 years ago
sun
▴ 100
3
votes
15
replies
3.5k
views
Are the p-values supposed to be on the order of 10^-120?
limma
affy
bioconductor
affymetrix
updated 11.0 years ago by
Gordon Smyth
53k • written 11.0 years ago by
mccallionc403
• 0
1
vote
3
replies
1.4k
views
id matching in select function within hugene10stprobeset.db
annotation
affy
annotationdbi
updated 11.0 years ago by
James W. MacDonald
68k • written 11.0 years ago by
sarose989
• 0
0
votes
2
replies
1.3k
views
RMA X prefix to Affymetrix annotations
microarray
affy
annotation
11.0 years ago
robin073
• 0
1
vote
1
reply
1.2k
views
analysing affymetrix experiment
affy
updated 11.1 years ago by
James W. MacDonald
68k • written 11.1 years ago by
Pau Marc Muñoz Torres
▴ 20
0
votes
2
replies
2.4k
views
HGU133Plus2 CDF vs hgu133plus2hsentrezgcdf CDF (30% difference in results)
GO
hgu133plus2
cdf
affy
limma
updated 11.1 years ago by
Steve Lianoglou
★ 13k • written 11.1 years ago by
Guest User
★ 13k
0
votes
5
replies
2.4k
views
Single sample normalization of single-channel Agilent microarrays
affy
frma
SCAN.UPC
affy
frma
SCAN.UPC
updated 11.1 years ago by
Ryan C. Thompson
★ 7.9k • written 11.1 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
Microarray data normalization
Normalization
GO
Cancer
probe
affy
Normalization
GO
Cancer
probe
affy
11.2 years ago
Levi Waldron
▴ 80
0
votes
3
replies
1.6k
views
Is a subset of my arrays from degraded RNA?
Microarray
GO
Clustering
affy
affyPLM
simpleaffy
Microarray
GO
Clustering
affy
affyPLM
11.2 years ago
Peter Davidsen
▴ 210
0
votes
6
replies
3.5k
views
processing Illumina HT12v4.0 expression data from GEO
Normalization
affy
PROcess
GEOquery
frma
Normalization
affy
PROcess
GEOquery
frma
updated 11.2 years ago by
Sean Davis
21k • written 11.2 years ago by
Abhishek Pratap
▴ 190
0
votes
6
replies
2.3k
views
SCAN.UPC for microarray and RNAseq data
RNASeq
affy
RNASeq
affy
updated 11.3 years ago by
Stephen Piccolo
▴ 600 • written 11.3 years ago by
shirley zhang
★ 1.0k
0
votes
6
replies
4.0k
views
converting probeset id to gene id's : fRMA
probe
affy
convert
frma
probe
affy
convert
frma
updated 11.3 years ago by
Peter Langfelder
★ 3.0k • written 11.3 years ago by
Abhishek Pratap
▴ 190
0
votes
1
reply
1.5k
views
Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe
affy
PROcess
oligo
probe
affy
PROcess
oligo
updated 11.3 years ago by
James W. MacDonald
68k • written 11.3 years ago by
Stephen Piccolo
▴ 600
0
votes
0
replies
767
views
affyxparser -- updating header information
affy
affy
11.4 years ago
Stacy Hung
▴ 10
0
votes
2
replies
2.0k
views
makecdfenv package bug
cdf
affy
affxparser
oligo
cdf
affy
affxparser
oligo
updated 11.4 years ago by
Danny Arends
▴ 10 • written 11.4 years ago by
James W. MacDonald
68k
0
votes
1
reply
1.1k
views
error in loading a bioconductor package affy
affy
affy
updated 11.4 years ago by
James W. MacDonald
68k • written 11.4 years ago by
Guest User
★ 13k
0
votes
4
replies
2.1k
views
combat error message
miRNA
Normalization
affy
miRNA
Normalization
affy
updated 11.4 years ago by
Guest User
★ 13k • written 11.4 years ago by
W. Evan Johnson
▴ 870
0
votes
1
reply
1.4k
views
oligo package - Unable to read HT-U133A CEL files
affy
oligo
affy
oligo
updated 11.4 years ago by
Benilton Carvalho
★ 4.3k • written 11.4 years ago by
Stephen Piccolo
▴ 600
0
votes
0
replies
1.3k
views
ComBat error message, thanks
miRNA
Normalization
affy
miRNA
Normalization
affy
11.5 years ago
Guan
▴ 20
0
votes
0
replies
3.7k
views
ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0
Normalization
Clustering
affy
Normalization
Clustering
affy
11.5 years ago
Guan
▴ 20
0
votes
5
replies
1.9k
views
Comparison of murine and human microarray data
Microarray
Normalization
affy
Microarray
Normalization
affy
updated 11.5 years ago by
Stephen Piccolo
▴ 600 • written 11.5 years ago by
Bas van Gestel
▴ 20
0
votes
4
replies
1.7k
views
GWASdata
SNP
affy
SNP
affy
11.5 years ago
Naomi Altman
★ 6.0k
0
votes
5
replies
1.9k
views
affy( ) error with mas5()
SNP
affy
PROcess
SNP
affy
PROcess
updated 11.5 years ago by
James W. MacDonald
68k • written 11.5 years ago by
Ying Chen
▴ 110
0
votes
2
replies
2.7k
views
make.cdf.package Error in copySubstitute
GO
cdf
Biobase
affy
GO
cdf
Biobase
affy
updated 11.6 years ago by
James W. MacDonald
68k • written 11.6 years ago by
matthew vitalone
▴ 30
0
votes
3
replies
1.4k
views
Library loading problem
affy
affy
updated 11.6 years ago by
Dan Tenenbaum
★ 8.2k • written 11.6 years ago by
prabhakar ghorpade
▴ 100
1
vote
1
reply
2.3k
views
Rosetta Resolver-like error-weighted ANOVAs in Bioconductor
Microarray
genefilter
affy
Microarray
genefilter
affy
updated 11.6 years ago by
Ryan C. Thompson
★ 7.9k • written 11.6 years ago by
Ida Hatoum
▴ 10
0
votes
2
replies
1.4k
views
Can we use Intraclass correlation (ICC) to optimize clustering parameters?
GO
Clustering
rat2302
affy
GO
Clustering
rat2302
affy
updated 11.7 years ago by
Tim Triche
★ 4.2k • written 11.7 years ago by
Guest User
★ 13k
0
votes
2
replies
1.4k
views
DAVIDQuery
Clustering
affy
Clustering
affy
updated 11.7 years ago by
Dan Tenenbaum
★ 8.2k • written 11.7 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
1.4k
views
Problem when trying to use \'affy\' package
Normalization
GO
affy
sva
SCAN.UPC
Normalization
GO
affy
sva
SCAN.UPC
11.7 years ago
Kaj Chokeshaiusaha
▴ 140
0
votes
3
replies
2.4k
views
how to extract probes for a probeset from PdInfo database?
miRNA
cdf
affy
miRNA
cdf
affy
updated 11.7 years ago by
Benilton Carvalho
★ 4.3k • written 11.7 years ago by
Guido Hooiveld
★ 4.1k
0
votes
0
replies
1.8k
views
Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
miRNA
cdf
affy
makecdfenv
affxparser
miRNA
cdf
affy
makecdfenv
affxparser
11.7 years ago
James W. MacDonald
68k
0
votes
9
replies
3.0k
views
using frma and brainarray cdf on exon arrays
cdf
affy
PROcess
oligo
xps
frma
cdf
affy
PROcess
oligo
xps
frma
updated 11.7 years ago by
Stephen Piccolo
▴ 600 • written 11.7 years ago by
Ty Thomson
▴ 100
1
vote
2
replies
2.2k
views
Help needed: extracting raw intensity values from Affy
probe
affy
gcrma
probe
affy
gcrma
updated 11.8 years ago by
shweta bagewadi
▴ 20 • written 11.8 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
2.5k
views
Importing RMA processed data into limma for eBayes
Microarray
Normalization
affy
vsn
limma
PROcess
xps
Microarray
Normalization
affy
vsn
11.8 years ago
Matthew Thornton
▴ 380
0
votes
1
reply
3.2k
views
Regarding R Package
affy
limma
affy
limma
updated 11.8 years ago by
Dan Tenenbaum
★ 8.2k • written 11.8 years ago by
«Jαyαηth¡.A»
▴ 10
0
votes
1
reply
2.3k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription
Annotation
Normalization
GO
hgu133plus2
affy
PROcess
Category
Transcription
updated 11.9 years ago by
Federico Lasa
▴ 80 • written 11.9 years ago by
María Maqueda González
▴ 20
0
votes
4
replies
4.4k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation
Normalization
hgu133plus2
affy
PROcess
Category
Annotation
Normalization
affy
updated 11.9 years ago by
James W. MacDonald
68k • written 11.9 years ago by
Guest User
★ 13k
0
votes
5
replies
2.2k
views
SCAN.UPC for Illumina arrays?
RNASeq
qPCR
affy
oligo
frma
RNASeq
qPCR
affy
oligo
frma
updated 11.9 years ago by
Stephen Piccolo
▴ 600 • written 11.9 years ago by
Tim Triche
★ 4.2k
0
votes
0
replies
1.4k
views
Farms/Call.INI using oligo package?
probe
affy
oligo
SIM
farms
probe
affy
oligo
SIM
farms
11.9 years ago
Djork Clevert
▴ 210
1,805 results • Page
5 of 37
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Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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