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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
9.6 years ago • updated 9.5 years ago
svlachavas
▴ 840
3
votes
15
replies
4.9k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
8.8 years ago
rasii
• 0
3
votes
14
replies
4.2k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools
qualitycontrol
HumanOmni5-4BeadChip
GenomeStudio
illumina
updated 8.7 years ago by
Stephanie M. Gogarten
▴ 890 • written 8.7 years ago by
Lna
• 0
6
votes
9
replies
1.8k
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 8.6 years ago by
Gordon Smyth
52k • written 8.6 years ago by
Konstantinos Yeles
▴ 80
4
votes
8
replies
11k
views
how to use idat file for analyses in bioconductor
microarray
illumina
idat
updated 8.9 years ago by
Gordon Smyth
52k • written 8.9 years ago by
kritikamish99
▴ 10
1
vote
7
replies
6.3k
views
convert fastq file to fasta using shortread package
illumina
shortread
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
kelvinfrog75
• 0
0
votes
7
replies
1.9k
views
getting error in processSwathData command from the beadarray package
microarray
beadarray
illumina
updated 9.8 years ago by
Mike Smith
★ 6.6k • written 9.8 years ago by
harpreet.saini
• 0
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 5.7 years ago by
Guido Hooiveld
★ 4.1k • written 5.7 years ago by
naf
• 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 9.4 years ago by
James W. MacDonald
67k • written 9.4 years ago by
kanacska
▴ 10
1
vote
6
replies
2.4k
views
Copy number analysis from Illumina 550K chip
illumina
copynumber
crlmm
9.2 years ago
stuti.agrawal
• 0
0
votes
6
replies
1.4k
views
Getting CDS positioning for IlluminaHumanv4 annotations
illumina
annotation
10.1 years ago
Sylvain Foisy
▴ 80
0
votes
6
replies
2.4k
views
Illumina bead array analysis
illumina
beadarray
updated 22 months ago by
Mark Dunning
★ 1.1k • written 10.3 years ago by
tomiptu
• 0
0
votes
6
replies
4.5k
views
How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
illumina
normalization
microarray
updated 9.5 years ago by
Mark Dunning
★ 1.1k • written 9.5 years ago by
kanacska
▴ 10
1
vote
5
replies
1.4k
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2
rna-seq
illumina
batch effect
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
JP Carter
▴ 40
4
votes
5
replies
3.1k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 9.6 years ago by
svlachavas
▴ 840 • written 9.6 years ago by
Agaz Hussain Wani
▴ 260
2
votes
5
replies
2.8k
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 3.1 years ago by
mohammedtoufiq91
▴ 10 • written 6.6 years ago by
Harpreet Kaur
• 0
11
votes
5
replies
2.6k
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 9.3 years ago by
Mark Cowley
▴ 400 • written 9.3 years ago by
willj
▴ 30
1
vote
5
replies
2.1k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm
illumina
beadarraysnp
updated 9.9 years ago by
Matthew Ritchie
▴ 1000 • written 9.9 years ago by
René
▴ 30
1
vote
4
replies
2.2k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 6.4 years ago by
James W. MacDonald
67k • written 6.4 years ago by
Alexander Azarian
▴ 30
2
votes
4
replies
1.5k
views
The error when using beadarry and limma packages for analysing illumina chip
limma
beadarray
illumina
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
261092095
▴ 10
1
vote
4
replies
1.1k
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
11 months ago
mikat
• 0
0
votes
4
replies
2.7k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina
annotation
updated 9.3 years ago by
Mike Smith
★ 6.6k • written 9.3 years ago by
kanacska
▴ 10
2
votes
4
replies
2.0k
views
read.idat function misleading error when reading compressed files
idat
illumina
limma
read.idat
updated 4.1 years ago by
Gordon Smyth
52k • written 4.1 years ago by
bastien_chassagnol
• 0
0
votes
4
replies
1.8k
views
minfi sample limit
minfi
illumina
illimina 450k methylation
methylation
updated 8.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.8 years ago by
igor
▴ 50
0
votes
4
replies
2.1k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db
aclust
methylation
annotation
illumina
updated 8.3 years ago by
b2cemaillist
• 0 • written 8.4 years ago by
aagata.szymanek
• 0
7
votes
4
replies
1.8k
views
very high adjusted P-vals using Illumina data from GEO
limma
p values
microarray
illumina
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
Jason
▴ 20
2
votes
3
replies
1.8k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 8.4 years ago by
Gordon Smyth
52k • written 8.4 years ago by
Stane
▴ 40
1
vote
3
replies
1.7k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
5.0 years ago
erwin.tomasich
▴ 10
0
votes
3
replies
2.5k
views
neqc normalization results in bimodal histogram of expression values
neqc
limma
microarray
illumina
updated 8.9 years ago by
Gordon Smyth
52k • written 8.9 years ago by
alexvpickering
▴ 110
0
votes
3
replies
2.1k
views
Error and warning message when reading the ballgown object
software error
illumina
DEG
ballgown
tuxedo
updated 6.8 years ago by
James W. MacDonald
67k • written 6.8 years ago by
amy16
• 0
0
votes
3
replies
1.7k
views
How can I pre-process illumina raw file
illumina
microarray
updated 7.4 years ago by
James W. MacDonald
67k • written 7.4 years ago by
Agaz Hussain Wani
▴ 260
1
vote
3
replies
1.7k
views
Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
7.5 years ago
ezrabekele17
• 0
2
votes
3
replies
2.8k
views
Normalization of Illumina Microarray Data
illumina
microarray
normalization
updated 7.8 years ago by
Gordon Smyth
52k • written 7.8 years ago by
paul.elliot1994
• 0
0
votes
3
replies
1.9k
views
MINFI missing samples in qcreports and densityplots
minfi
illumina
methylationEPIC
densityplot
8.0 years ago
annabelle.congras
▴ 10
0
votes
2
replies
1.3k
views
BAM file into R from Illumina
bam file
STAR
Illumina
updated 6.7 years ago by
ta_awwad
▴ 10 • written 6.7 years ago by
soheilazareie
• 0
4
votes
2
replies
5.0k
views
gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
illumina
updated 10.2 years ago by
James W. MacDonald
67k • written 10.2 years ago by
Li Liu
▴ 100
0
votes
2
replies
2.1k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray
illumina
methylation
microarray
updated 9.3 years ago by
Sean Davis
21k • written 9.3 years ago by
maria.keays
• 0
1
vote
2
replies
1.6k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 6.1 years ago by
Ou, Jianhong
★ 1.3k • written 6.1 years ago by
Adam_M
• 0
0
votes
2
replies
1.4k
views
permutation with plink
illumina
plink
permutation
updated 8.6 years ago by
James W. MacDonald
67k • written 8.6 years ago by
sedrinne
• 0
1
vote
2
replies
1.7k
views
minfi package QC report error?
minfi
methylation
illumina
10.2 years ago
Brian Smith
▴ 120
0
votes
2
replies
1.1k
views
Error myDMP not found
Illumina
methylationArrayAnalysis
ChAMPdata
ChAMP
4.0 years ago
sissialva21
• 0
0
votes
2
replies
5.9k
views
How to read bgx files in R
microarray
annotation
illumina
9.5 years ago
kanacska
▴ 10
2
votes
2
replies
1.8k
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 9.6 years ago by
Mike Smith
★ 6.6k • written 9.6 years ago by
svlachavas
▴ 840
0
votes
2
replies
1.5k
views
clustering analysis of illumina microarray gene expression data
clustering
illumina
microarray
8.9 years ago
kritikamish99
▴ 10
0
votes
2
replies
2.2k
views
Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
minfi
minfidata
illumina
methylation
dmpfinder
updated 10.3 years ago by
James W. MacDonald
67k • written 10.3 years ago by
michael.zulyniak
• 0
0
votes
2
replies
2.3k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 7.7 years ago by
Guido Hooiveld
★ 4.1k • written 7.7 years ago by
Ellen O
• 0
0
votes
2
replies
1.5k
views
ShortRead summary stats
shortread
illumina
9.8 years ago
danova_fr
▴ 20
1
vote
1
reply
1.4k
views
PCA input data from DRAGEN RNA pipeline
illumina
PCAtools
PCA
updated 2.2 years ago by
Kevin Blighe
★ 4.0k • written 2.2 years ago by
ilaria.debenedictis
• 0
0
votes
1
reply
1.8k
views
Error regarding installation and loading of "Lumi" Package
software error
microarray
illumina
updated 10.0 years ago by
Steve Lianoglou
★ 13k • written 10.0 years ago by
Deeksha Malhan
▴ 10
1
vote
1
reply
1.5k
views
Error genotyping with CRLMM
crlmm
copynumber
illumina
updated 9.2 years ago by
andrew.j.skelton73
▴ 370 • written 9.2 years ago by
stuti.agrawal
• 0
50 results • Page
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
by
James W. MacDonald
67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue
by
k.panov
• 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package
by
Lukas
▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts
by
sindhuri
• 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package
by
James W. MacDonald
67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
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Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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