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illumina
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18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
9.7 years ago • updated 9.6 years ago
svlachavas
▴ 840
4
votes
8
replies
12k
views
how to use idat file for analyses in bioconductor
microarray
illumina
idat
updated 9.0 years ago by
Gordon Smyth
52k • written 9.0 years ago by
kritikamish99
▴ 10
1
vote
7
replies
6.4k
views
convert fastq file to fasta using shortread package
illumina
shortread
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
kelvinfrog75
• 0
0
votes
2
replies
6.0k
views
How to read bgx files in R
microarray
annotation
illumina
9.6 years ago
kanacska
▴ 10
3
votes
15
replies
5.0k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
8.9 years ago
rasii
• 0
4
votes
2
replies
5.0k
views
gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
illumina
updated 10.3 years ago by
James W. MacDonald
68k • written 10.3 years ago by
Li Liu
▴ 100
0
votes
6
replies
4.6k
views
How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
illumina
normalization
microarray
updated 9.6 years ago by
Mark Dunning
★ 1.1k • written 9.6 years ago by
kanacska
▴ 10
3
votes
14
replies
4.3k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools
qualitycontrol
HumanOmni5-4BeadChip
GenomeStudio
illumina
updated 8.8 years ago by
Stephanie M. Gogarten
▴ 890 • written 8.8 years ago by
Lna
• 0
4
votes
5
replies
3.2k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 9.7 years ago by
svlachavas
▴ 840 • written 9.7 years ago by
Agaz Hussain Wani
▴ 260
2
votes
5
replies
2.9k
views
Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
limma
lumi
illumina
gene expression data
updated 3.2 years ago by
mohammedtoufiq91
▴ 10 • written 6.7 years ago by
Harpreet Kaur
• 0
2
votes
3
replies
2.8k
views
Normalization of Illumina Microarray Data
illumina
microarray
normalization
updated 7.9 years ago by
Gordon Smyth
52k • written 8.0 years ago by
paul.elliot1994
• 0
3
votes
6
replies
2.8k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma
illumina
microarray
lmfit
differential gene expression
updated 9.6 years ago by
James W. MacDonald
68k • written 9.6 years ago by
kanacska
▴ 10
0
votes
4
replies
2.8k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina
annotation
updated 9.4 years ago by
Mike Smith
★ 6.6k • written 9.4 years ago by
kanacska
▴ 10
0
votes
0
replies
2.7k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi
illumina
normalization
beadarray
7.8 years ago
hkarakurt
▴ 20
11
votes
5
replies
2.7k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat
idat
microarray
illumina
updated 9.4 years ago by
Mark Cowley
▴ 400 • written 9.4 years ago by
willj
▴ 30
0
votes
3
replies
2.5k
views
neqc normalization results in bimodal histogram of expression values
neqc
limma
microarray
illumina
updated 9.0 years ago by
Gordon Smyth
52k • written 9.0 years ago by
alexvpickering
▴ 110
0
votes
6
replies
2.5k
views
Illumina bead array analysis
illumina
beadarray
updated 24 months ago by
Mark Dunning
★ 1.1k • written 10.4 years ago by
tomiptu
• 0
0
votes
1
reply
2.5k
views
Question about neqc and GEO illumina files
neqc
illumina
geo
limma
updated 8.7 years ago by
Gordon Smyth
52k • written 8.7 years ago by
akridgerunner
▴ 30
0
votes
7
replies
2.4k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix
Illumina
probes
microarray
annotation package
updated 5.8 years ago by
Guido Hooiveld
★ 4.1k • written 5.8 years ago by
naf
• 0
1
vote
6
replies
2.4k
views
Copy number analysis from Illumina 550K chip
illumina
copynumber
crlmm
9.3 years ago
stuti.agrawal
• 0
0
votes
2
replies
2.4k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 7.8 years ago by
Guido Hooiveld
★ 4.1k • written 7.8 years ago by
Ellen O
• 0
1
vote
4
replies
2.2k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 6.5 years ago by
James W. MacDonald
68k • written 6.5 years ago by
Alexander Azarian
▴ 30
0
votes
2
replies
2.2k
views
Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
minfi
minfidata
illumina
methylation
dmpfinder
updated 10.4 years ago by
James W. MacDonald
68k • written 10.4 years ago by
michael.zulyniak
• 0
1
vote
5
replies
2.1k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm
illumina
beadarraysnp
updated 10.0 years ago by
Matthew Ritchie
▴ 1000 • written 10.0 years ago by
René
▴ 30
0
votes
3
replies
2.1k
views
Error and warning message when reading the ballgown object
software error
illumina
DEG
ballgown
tuxedo
updated 6.9 years ago by
James W. MacDonald
68k • written 6.9 years ago by
amy16
• 0
0
votes
4
replies
2.1k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db
aclust
methylation
annotation
illumina
updated 8.4 years ago by
b2cemaillist
• 0 • written 8.5 years ago by
aagata.szymanek
• 0
1
vote
1
reply
2.1k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names
methylation
illumina
convertids
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
arbet003
▴ 10
0
votes
2
replies
2.1k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray
illumina
methylation
microarray
updated 9.4 years ago by
Sean Davis
21k • written 9.4 years ago by
maria.keays
• 0
2
votes
4
replies
2.0k
views
read.idat function misleading error when reading compressed files
idat
illumina
limma
read.idat
updated 4.2 years ago by
Gordon Smyth
52k • written 4.2 years ago by
bastien_chassagnol
• 0
0
votes
3
replies
2.0k
views
MINFI missing samples in qcreports and densityplots
minfi
illumina
methylationEPIC
densityplot
8.1 years ago
annabelle.congras
▴ 10
0
votes
0
replies
1.9k
views
Any alternative to GenomeStudio to analyze Illumina VeraCode arrays? Is Beadarray an option?
microarray
beadarray
Illumina
Veracode
10.1 years ago
lacion
• 0
0
votes
7
replies
1.9k
views
getting error in processSwathData command from the beadarray package
microarray
beadarray
illumina
updated 9.9 years ago by
Mike Smith
★ 6.6k • written 9.9 years ago by
harpreet.saini
• 0
7
votes
4
replies
1.9k
views
very high adjusted P-vals using Illumina data from GEO
limma
p values
microarray
illumina
updated 9.1 years ago by
James W. MacDonald
68k • written 9.1 years ago by
Jason
▴ 20
6
votes
9
replies
1.9k
views
Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma
illumina
microarray
multifactorial design
batch effect
updated 8.7 years ago by
Gordon Smyth
52k • written 8.7 years ago by
Konstantinos Yeles
▴ 80
2
votes
2
replies
1.9k
views
Annotation problems regarding quality information for Illumina HumanHT-12 v4-illuminaHumanv4.db
illumina human ht-12 v4
illuminahumanv4.db
filtering on probe annotation
illumina
updated 9.7 years ago by
Mike Smith
★ 6.6k • written 9.7 years ago by
svlachavas
▴ 840
0
votes
1
reply
1.8k
views
Error in Matrix
minfi
methylation
EPIC microarray
illumina
updated 8.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.8 years ago by
rasii
• 0
0
votes
4
replies
1.8k
views
minfi sample limit
minfi
illumina
illimina 450k methylation
methylation
updated 8.9 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.9 years ago by
igor
▴ 50
0
votes
1
reply
1.8k
views
Error regarding installation and loading of "Lumi" Package
software error
microarray
illumina
updated 10.1 years ago by
Steve Lianoglou
★ 13k • written 10.1 years ago by
Deeksha Malhan
▴ 10
1
vote
1
reply
1.8k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm
gsa
microarray
illumina
written 6.8 years ago by
shaun
• 0
1
vote
3
replies
1.8k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
5.1 years ago
erwin.tomasich
▴ 10
2
votes
3
replies
1.8k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 8.5 years ago by
Gordon Smyth
52k • written 8.5 years ago by
Stane
▴ 40
1
vote
2
replies
1.7k
views
minfi package QC report error?
minfi
methylation
illumina
10.3 years ago
Brian Smith
▴ 120
0
votes
3
replies
1.7k
views
How can I pre-process illumina raw file
illumina
microarray
updated 7.5 years ago by
James W. MacDonald
68k • written 7.5 years ago by
Agaz Hussain Wani
▴ 260
0
votes
0
replies
1.7k
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads
methylation
illumina
epic microarray
8.5 years ago
rasii
• 0
2
votes
1
reply
1.7k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina
bioconductor
limma
microarray
normalization
updated 9.3 years ago by
Gordon Smyth
52k • written 9.3 years ago by
Konstantinos Yeles
▴ 80
2
votes
1
reply
1.7k
views
Differential Expression Analysis
differential gene expression
microarray
lumi
illumina
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
paul.elliot1994
• 0
1
vote
3
replies
1.7k
views
Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
7.6 years ago
ezrabekele17
• 0
1
vote
1
reply
1.7k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 7.3 years ago by
k.vitting.seerup
▴ 120 • written 7.3 years ago by
amy16
• 0
1
vote
2
replies
1.7k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 6.2 years ago by
Ou, Jianhong
★ 1.3k • written 6.2 years ago by
Adam_M
• 0
0
votes
1
reply
1.6k
views
Problems in using lumi for importing illumina raw data
beadarray
lumi
normalization
microarray
illumina
updated 8.2 years ago by
Gordon Smyth
52k • written 8.2 years ago by
Biologist
▴ 120
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Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
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Thank you
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Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
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