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beadarray
•
reset
2
votes
4
replies
1.3k
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis
illuminaio
beadarray
DSS
bsseqData
2.3 years ago
Jojo
• 0
0
votes
1
reply
679
views
readIDAT output to beadarray package input file
Beadarray
readIDAT
updated 2.4 years ago by
James W. MacDonald
65k • written 2.4 years ago by
Đạt
• 0
1
vote
3
replies
920
views
Help with the beadarray package
IlluminaChip
beadarray
updated 2.6 years ago by
Gordon Smyth
50k • written 2.6 years ago by
noa.gilat
• 0
0
votes
1
reply
821
views
How to extract DEG from limmarResults object after beadarray analysis
beadarray
limma
updated 2.8 years ago by
Gordon Smyth
50k • written 2.8 years ago by
curiousmind007
▴ 10
3
votes
1
reply
973
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray
GSE22247
limma
GEOquery
IlluminaChip
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
bastien_chassagnol
• 0
3
votes
1
reply
875
views
How to convert dataframe into ExpressionSetIllumina / summarized data with beadarray package?
beadarray
updated 4.5 years ago by
Mark Dunning
★ 1.1k • written 4.5 years ago by
salamandra
▴ 20
1
vote
3
replies
2.5k
views
Installing arrayQualityMetrics: ERROR: lazy loading failed
arrayqualitymetrics
beadarray
7.9 years ago • updated 4.8 years ago
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
1.3k
views
cram for new chips
beadarray
illumina beadarray
crlmm
updated 5.9 years ago by
Valerie Obenchain
★ 6.8k • written 5.9 years ago by
lack.justin
• 0
2
votes
4
replies
1.3k
views
The error when using beadarry and limma packages for analysing illumina chip
limma
beadarray
illumina
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
261092095
▴ 10
0
votes
5
replies
1.8k
views
Probe summerization of Human HT-12 V4 BeadChip arrays
beadarray
bead chip
illuminahumanv4.db
normalization
RMA
updated 6.5 years ago by
James W. MacDonald
65k • written 6.5 years ago by
Seymoo
• 0
0
votes
2
replies
1.2k
views
beadsummary example- Analysing data from GEO
beadarray
7.1 years ago • updated 7.0 years ago
anna.katsiki
• 0
0
votes
4
replies
1.7k
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 7.0 years ago by
Mark Dunning
★ 1.1k • written 7.1 years ago by
S. K.
• 0
0
votes
0
replies
2.5k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi
illumina
normalization
beadarray
7.0 years ago
hkarakurt
▴ 20
0
votes
1
reply
1.1k
views
beadarray: summarizing iScan data is not working
beadarray
iscan
7.1 years ago
S. K.
• 0
0
votes
0
replies
1.0k
views
beadarray: Make grep in readSamplesheet case insensitive
beadarray
bug
7.1 years ago
S. K.
• 0
0
votes
1
reply
1.4k
views
Problems in using lumi for importing illumina raw data
beadarray
lumi
normalization
microarray
illumina
updated 7.4 years ago by
Gordon Smyth
50k • written 7.4 years ago by
Biologist
▴ 110
0
votes
1
reply
937
views
beadarray error conversion
beadarray
limma
ExpressionSet
updated 7.4 years ago by
Gordon Smyth
50k • written 7.4 years ago by
emiliomastriani
• 0
0
votes
7
replies
2.3k
views
Bioconductor 2.6 is released
Sequencing
Microarray
Visualization
Infrastructure
PROcess
beadarray
keggorthology
eisa
updated 7.7 years ago by
wangyizhusss
• 0 • written 14.1 years ago by
Patrick Aboyoun
★ 1.6k
0
votes
1
reply
1.0k
views
Processing iScan raw data without perBeadFile.txt
microarray
beadarray
updated 8.1 years ago by
Mike Smith
★ 6.5k • written 8.1 years ago by
aizhang
• 0
1
vote
2
replies
1.4k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray
bead-level
GEO
lumi
updated 8.2 years ago by
Mike Smith
★ 6.5k • written 8.2 years ago by
gnilihzeux
• 0
3
votes
12
replies
6.2k
views
packages installation problem
limma
Rqc
beadarray
Lumi
updated 8.3 years ago by
Welliton de Souza
▴ 70 • written 8.3 years ago by
raya.girish
• 0
0
votes
0
replies
1.3k
views
Can beadarray package process SNP normalization and genotype calling?
beadarray
8.3 years ago
zhuyeqingting
• 0
0
votes
2
replies
2.0k
views
Beadarray import of iScan generated Illumina gene expression data
Microarray
GO
ChipName
beadarray
Microarray
GO
ChipName
beadarray
updated 8.3 years ago by
zhuyeqingting
• 0 • written 12.5 years ago by
Aliaksei Holik
▴ 350
0
votes
2
replies
1.8k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray
illumina
methylation
microarray
updated 8.6 years ago by
Sean Davis
21k • written 8.6 years ago by
maria.keays
• 0
4
votes
10
replies
2.2k
views
Zero values for bead backgrounds (reading idat files using Illuminaio)
illuminaio
idat
beadarray
updated 8.7 years ago by
Mike Smith
★ 6.5k • written 8.7 years ago by
willj
▴ 30
0
votes
7
replies
1.6k
views
getting error in processSwathData command from the beadarray package
microarray
beadarray
illumina
updated 9.2 years ago by
Mike Smith
★ 6.5k • written 9.2 years ago by
harpreet.saini
• 0
0
votes
3
replies
2.6k
views
Problem with reading raw Illumina Human HT-12 v4 data using beadarray
beadarray
readIllumina
9.2 years ago
jaro.slamecka
▴ 140
0
votes
1
reply
1.2k
views
Fail to read qcFile in readBeadSummaryData function
beadarray
updated 9.3 years ago by
meeta.mistry
▴ 30 • written 9.4 years ago by
junjeong
• 0
0
votes
0
replies
1.3k
views
beadarray - QC file loads but doesn't appear in ExpressionSetIllumina object
beadarray
qc
9.3 years ago
meeta.mistry
▴ 30
0
votes
0
replies
1.8k
views
Any alternative to GenomeStudio to analyze Illumina VeraCode arrays? Is Beadarray an option?
microarray
beadarray
Illumina
Veracode
9.3 years ago
lacion
• 0
0
votes
6
replies
2.2k
views
Illumina bead array analysis
illumina
beadarray
updated 14 months ago by
Mark Dunning
★ 1.1k • written 9.6 years ago by
tomiptu
• 0
0
votes
3
replies
1.5k
views
unable to set sampleNames after combine (from beadarray package) on ExpressionSetIllumina
beadarray
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
Adaikalavan Ramasamy
▴ 220
0
votes
3
replies
1.7k
views
sampleSheet problem in beadArray
beadarray
beadarray
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Guest User
★ 13k
0
votes
0
replies
1.3k
views
crlmm problem
SNP
convert
beadarray
crlmm
SNP
convert
beadarray
crlmm
10.2 years ago
Matthias Arnold
▴ 10
0
votes
1
reply
2.7k
views
Normalization of Illumina Array with separate bgx-file
Annotation
limma
beadarray
bgx
Annotation
limma
beadarray
bgx
updated 10.3 years ago by
Gordon Smyth
50k • written 10.3 years ago by
Stefanie Busch
▴ 10
0
votes
2
replies
1.5k
views
crlmm problem
SNP
beadarray
crlmm
SNP
beadarray
crlmm
10.3 years ago
Aaerp
▴ 40
0
votes
1
reply
2.0k
views
hoeffd function (CRAN HMisc package) use in arrayQualityMetrics
beadarray
beadarray
updated 10.4 years ago by
Wolfgang Huber
★ 13k • written 10.4 years ago by
Guest User
★ 13k
0
votes
0
replies
1.8k
views
Illumina Expression analysis from iDAT files
Normalization
limma
beadarray
lumi
illuminaio
Normalization
limma
beadarray
lumi
10.5 years ago
Kasper Daniel Hansen
★ 6.5k
3
votes
9
replies
5.7k
views
Illumina Expression analysis from iDAT files
beadarray
lumi
illuminaio
idat
updated 2.4 years ago by
Gordon Smyth
50k • written 10.5 years ago by
Sean Davis
21k
0
votes
1
reply
1.0k
views
beadarray library: perBeadFile
GLAD
beadarray
GLAD
beadarray
updated 10.8 years ago by
Mike Smith
★ 6.5k • written 10.8 years ago by
Nogales Vilardell
▴ 10
0
votes
9
replies
1.9k
views
beadarray - combining swath files
PROcess
beadarray
PROcess
beadarray
updated 11.0 years ago by
Mark Dunning
★ 1.1k • written 11.0 years ago by
Darren Plant
▴ 70
0
votes
0
replies
1.4k
views
using beadarray to process iscan expression data - error using readIllumina()
PROcess
beadarray
PROcess
beadarray
11.0 years ago
Darren Plant
▴ 70
0
votes
0
replies
1.3k
views
How do I background correct an Illumina eset without using lumiB
Microarray
probe
limma
PROcess
convert
beadarray
lumi
Microarray
probe
limma
PROcess
11.0 years ago
Gordon Smyth
50k
0
votes
1
reply
1.3k
views
How do I background correct an Illumina eset without using lumiB?
Microarray
probe
PROcess
convert
beadarray
lumi
Microarray
probe
PROcess
convert
lumi
updated 11.0 years ago by
Pan Du
▴ 440 • written 11.0 years ago by
Guest User
★ 13k
0
votes
1
reply
1.2k
views
ABarray error
Microarray
Annotation
GO
limma
beadarray
Microarray
Annotation
GO
limma
beadarray
11.1 years ago • updated 11.0 years ago
Mani, Jay
▴ 20
0
votes
0
replies
896
views
beadarray - combining swath files
beadarray
beadarray
11.2 years ago
Sunitha M
▴ 20
0
votes
0
replies
914
views
Beadarray - combining the 2 swath files
beadarray
beadarray
11.2 years ago
Sunitha M
▴ 20
0
votes
1
reply
4.0k
views
Problem installing packages on new R
limma
beadarray
lumi
arrayMvout
limma
beadarray
lumi
arrayMvout
updated 11.3 years ago by
James W. MacDonald
65k • written 11.3 years ago by
v.leoncikas@surrey.ac.uk
▴ 10
0
votes
0
replies
993
views
Fwd: iScan
beadarray
beadarray
11.3 years ago
Rajasree Menon
▴ 30
0
votes
2
replies
1.3k
views
Generating GEO submission files from beadarray summary data
beadarray
lumi
PROMISE
beadarray
lumi
PROMISE
updated 11.6 years ago by
Mark Dunning
★ 1.1k • written 11.6 years ago by
Tim Triche
★ 4.2k
50 results • Page
1 of 1
Recent ...
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Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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