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Showing :
beadarray
•
reset
2
votes
4
replies
476
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis
illuminaio
beadarray
DSS
bsseqData
12 months ago
Jojo
• 0
0
votes
1
reply
329
views
readIDAT output to beadarray package input file
Beadarray
readIDAT
updated 14 months ago by
James W. MacDonald
62k • written 14 months ago by
Đạt
• 0
1
vote
3
replies
477
views
Help with the beadarray package
IlluminaChip
beadarray
updated 15 months ago by
Gordon Smyth
47k • written 15 months ago by
noa.gilat
• 0
0
votes
1
reply
416
views
How to extract DEG from limmarResults object after beadarray analysis
beadarray
limma
updated 18 months ago by
Gordon Smyth
47k • written 18 months ago by
curiousmind007
• 0
3
votes
1
reply
473
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray
GSE22247
limma
GEOquery
IlluminaChip
updated 2.1 years ago by
Gordon Smyth
47k • written 2.1 years ago by
bastien_chassagnol
• 0
3
votes
1
reply
519
views
How to convert dataframe into ExpressionSetIllumina / summarized data with beadarray package?
beadarray
updated 3.2 years ago by
Mark Dunning
★ 1.1k • written 3.2 years ago by
salamandra
▴ 20
1
vote
3
replies
1.9k
views
Installing arrayQualityMetrics: ERROR: lazy loading failed
arrayqualitymetrics
beadarray
6.6 years ago • updated 3.6 years ago
Lluís Revilla Sancho
▴ 700
0
votes
3
replies
784
views
cram for new chips
beadarray
illumina beadarray
crlmm
updated 4.6 years ago by
Valerie Obenchain
★ 6.7k • written 4.6 years ago by
lack.justin
• 0
2
votes
4
replies
811
views
The error when using beadarry and limma packages for analysing illumina chip
limma
beadarray
illumina
updated 4.7 years ago by
Gordon Smyth
47k • written 4.7 years ago by
261092095
▴ 10
0
votes
5
replies
1.2k
views
Probe summerization of Human HT-12 V4 BeadChip arrays
beadarray
bead chip
illuminahumanv4.db
normalization
RMA
updated 5.2 years ago by
James W. MacDonald
62k • written 5.2 years ago by
Seymoo
• 0
0
votes
2
replies
786
views
beadsummary example- Analysing data from GEO
beadarray
5.8 years ago • updated 5.7 years ago
anna.katsiki
• 0
0
votes
4
replies
1.3k
views
beadarray: readIllumina with sample sheet broken due to Illumina switching to 12 digit chip identifiers
beadarray
bug
illumina human ht-12 v4
illumina beadchip
updated 5.7 years ago by
Mark Dunning
★ 1.1k • written 5.8 years ago by
S. K.
• 0
0
votes
0
replies
1.9k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi
illumina
normalization
beadarray
5.7 years ago
hkarakurt
▴ 20
0
votes
1
reply
773
views
beadarray: summarizing iScan data is not working
beadarray
iscan
5.8 years ago
S. K.
• 0
0
votes
0
replies
802
views
beadarray: Make grep in readSamplesheet case insensitive
beadarray
bug
5.8 years ago
S. K.
• 0
0
votes
1
reply
850
views
Problems in using lumi for importing illumina raw data
beadarray
lumi
normalization
microarray
illumina
updated 6.1 years ago by
Gordon Smyth
47k • written 6.1 years ago by
Biologist
▴ 110
0
votes
1
reply
631
views
beadarray error conversion
beadarray
limma
ExpressionSet
updated 6.1 years ago by
Gordon Smyth
47k • written 6.1 years ago by
emiliomastriani
• 0
0
votes
7
replies
1.6k
views
Bioconductor 2.6 is released
Sequencing
Microarray
Visualization
Infrastructure
PROcess
beadarray
keggorthology
eisa
updated 6.4 years ago by
wangyizhusss
• 0 • written 12.8 years ago by
Patrick Aboyoun
1.6k
0
votes
1
reply
796
views
Processing iScan raw data without perBeadFile.txt
microarray
beadarray
updated 6.8 years ago by
Mike Smith
★ 5.9k • written 6.8 years ago by
aizhang
• 0
1
vote
2
replies
1.0k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray
bead-level
GEO
lumi
updated 6.9 years ago by
Mike Smith
★ 5.9k • written 6.9 years ago by
gnilihzeux
• 0
3
votes
12
replies
5.2k
views
packages installation problem
limma
Rqc
beadarray
Lumi
updated 7.0 years ago by
Welliton de Souza
▴ 70 • written 7.0 years ago by
raya.girish
• 0
0
votes
0
replies
1.0k
views
Can beadarray package process SNP normalization and genotype calling?
beadarray
7.0 years ago
zhuyeqingting
• 0
0
votes
2
replies
1.6k
views
Beadarray import of iScan generated Illumina gene expression data
Microarray
GO
ChipName
beadarray
Microarray
GO
ChipName
beadarray
updated 7.0 years ago by
zhuyeqingting
• 0 • written 11.2 years ago by
Aliaksei Holik
▴ 350
0
votes
2
replies
1.5k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray
illumina
methylation
microarray
updated 7.3 years ago by
Sean Davis
21k • written 7.3 years ago by
maria.keays
• 0
4
votes
10
replies
1.5k
views
Zero values for bead backgrounds (reading idat files using Illuminaio)
illuminaio
idat
beadarray
updated 7.4 years ago by
Mike Smith
★ 5.9k • written 7.4 years ago by
willj
▴ 30
0
votes
7
replies
1.2k
views
getting error in processSwathData command from the beadarray package
microarray
beadarray
illumina
updated 7.9 years ago by
Mike Smith
★ 5.9k • written 7.9 years ago by
harpreet.saini
• 0
0
votes
3
replies
2.3k
views
Problem with reading raw Illumina Human HT-12 v4 data using beadarray
beadarray
readIllumina
7.9 years ago
jaro.slamecka
▴ 130
0
votes
1
reply
886
views
Fail to read qcFile in readBeadSummaryData function
beadarray
updated 8.0 years ago by
meeta.mistry
▴ 30 • written 8.1 years ago by
junjeong
• 0
0
votes
0
replies
972
views
beadarray - QC file loads but doesn't appear in ExpressionSetIllumina object
beadarray
qc
8.0 years ago
meeta.mistry
▴ 30
0
votes
0
replies
1.5k
views
Any alternative to GenomeStudio to analyze Illumina VeraCode arrays? Is Beadarray an option?
microarray
beadarray
Illumina
Veracode
8.0 years ago
lacion
• 0
0
votes
3
replies
1.6k
views
Illumina bead array analysis
illumina
beadarray
updated 8.4 years ago by
Mike Smith
★ 5.9k • written 8.4 years ago by
tomiptu
• 0
0
votes
3
replies
1.2k
views
unable to set sampleNames after combine (from beadarray package) on ExpressionSetIllumina
beadarray
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
Adaikalavan Ramasamy
▴ 220
0
votes
3
replies
1.3k
views
sampleSheet problem in beadArray
beadarray
beadarray
updated 8.5 years ago by
James W. MacDonald
62k • written 8.5 years ago by
Guest User
★ 12k
0
votes
0
replies
994
views
crlmm problem
SNP
convert
beadarray
crlmm
SNP
convert
beadarray
crlmm
8.9 years ago
Matthias Arnold
▴ 10
0
votes
1
reply
2.2k
views
Normalization of Illumina Array with separate bgx-file
Annotation
limma
beadarray
bgx
Annotation
limma
beadarray
bgx
updated 9.0 years ago by
Gordon Smyth
47k • written 9.0 years ago by
Stefanie Busch
▴ 10
0
votes
2
replies
1.1k
views
crlmm problem
SNP
beadarray
crlmm
SNP
beadarray
crlmm
9.0 years ago
Aaerp
▴ 40
0
votes
1
reply
1.5k
views
hoeffd function (CRAN HMisc package) use in arrayQualityMetrics
beadarray
beadarray
updated 9.1 years ago by
Wolfgang Huber
13k • written 9.2 years ago by
Guest User
★ 12k
0
votes
0
replies
1.5k
views
Illumina Expression analysis from iDAT files
Normalization
limma
beadarray
lumi
illuminaio
Normalization
limma
beadarray
lumi
9.2 years ago
Kasper Daniel Hansen
6.5k
3
votes
9
replies
4.6k
views
Illumina Expression analysis from iDAT files
beadarray
lumi
illuminaio
idat
updated 14 months ago by
Gordon Smyth
47k • written 9.2 years ago by
Sean Davis
21k
0
votes
1
reply
759
views
beadarray library: perBeadFile
GLAD
beadarray
GLAD
beadarray
updated 9.5 years ago by
Mike Smith
★ 5.9k • written 9.5 years ago by
Nogales Vilardell
▴ 10
0
votes
9
replies
1.3k
views
beadarray - combining swath files
PROcess
beadarray
PROcess
beadarray
updated 9.7 years ago by
Mark Dunning
★ 1.1k • written 9.7 years ago by
Darren Plant
▴ 70
0
votes
0
replies
1.1k
views
using beadarray to process iscan expression data - error using readIllumina()
PROcess
beadarray
PROcess
beadarray
9.7 years ago
Darren Plant
▴ 70
0
votes
0
replies
1.0k
views
How do I background correct an Illumina eset without using lumiB
Microarray
probe
limma
PROcess
convert
beadarray
lumi
Microarray
probe
limma
PROcess
9.7 years ago
Gordon Smyth
47k
0
votes
1
reply
1.1k
views
How do I background correct an Illumina eset without using lumiB?
Microarray
probe
PROcess
convert
beadarray
lumi
Microarray
probe
PROcess
convert
lumi
updated 9.7 years ago by
Pan Du
▴ 440 • written 9.7 years ago by
Guest User
★ 12k
0
votes
1
reply
876
views
ABarray error
Microarray
Annotation
GO
limma
beadarray
Microarray
Annotation
GO
limma
beadarray
9.8 years ago
Mani, Jay
▴ 20
0
votes
0
replies
677
views
beadarray - combining swath files
beadarray
beadarray
9.9 years ago
Sunitha M
▴ 20
0
votes
0
replies
682
views
Beadarray - combining the 2 swath files
beadarray
beadarray
9.9 years ago
Sunitha M
▴ 20
0
votes
1
reply
3.2k
views
Problem installing packages on new R
limma
beadarray
lumi
arrayMvout
limma
beadarray
lumi
arrayMvout
updated 10.0 years ago by
James W. MacDonald
62k • written 10.0 years ago by
v.leoncikas@surrey.ac.uk
▴ 10
0
votes
0
replies
750
views
Fwd: iScan
beadarray
beadarray
10.0 years ago
Rajasree Menon
▴ 30
0
votes
2
replies
938
views
Generating GEO submission files from beadarray summary data
beadarray
lumi
PROMISE
beadarray
lumi
PROMISE
updated 10.3 years ago by
Mark Dunning
★ 1.1k • written 10.3 years ago by
Tim Triche
★ 4.2k
50 results • Page
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Answer: struggling to create a heatmap
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ATpoint
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I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
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39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
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ATpoint
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That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
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You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
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Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
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