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illumina
•
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0
votes
0
replies
51
views
Annotation Illumina Infinium Mouse Methylation
Illumina
minfi
IlluminaHumanMethylationEPICmanifest
27 days ago
octaviompa
• 0
0
votes
2
replies
377
views
Error myDMP not found
Illumina
methylationArrayAnalysis
ChAMPdata
ChAMP
15 months ago
sissialva21
• 0
2
votes
4
replies
592
views
read.idat function misleading error when reading compressed files
idat
illumina
limma
read.idat
updated 17 months ago by
Gordon Smyth
45k • written 17 months ago by
bastien_chassagnol
• 0
1
vote
3
replies
488
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
2.3 years ago
erwin.tomasich
▴ 10
0
votes
7
replies
780
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix
Illumina
probes
microarray
annotation package
updated 3.0 years ago by
Guido Hooiveld
★ 3.2k • written 3.0 years ago by
naf
• 0
1
vote
2
replies
778
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 3.4 years ago by
Ou, Jianhong
★ 1.3k • written 3.4 years ago by
Adam_M
• 0
1
vote
4
replies
1.1k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 3.7 years ago by
James W. MacDonald
59k • written 3.8 years ago by
Alexander Azarian
▴ 30
2
votes
5
replies
1.1k
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 5 months ago by
mohammedtoufiq91
▴ 10 • written 3.9 years ago by
hks04180
• 0
2
votes
4
replies
661
views
The error when using beadarry and limma packages for analysing illumina chip
limma
beadarray
illumina
updated 3.9 years ago by
Gordon Smyth
45k • written 3.9 years ago by
261092095
▴ 10
1
vote
1
reply
877
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names
methylation
illumina
convertids
updated 4.0 years ago by
James W. MacDonald
59k • written 4.0 years ago by
arbet003
▴ 10
1
vote
1
reply
752
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm
gsa
microarray
illumina
updated 4.0 years ago by
funnyjokes1.com
• 0 • written 4.0 years ago by
shaun
• 0
1
vote
5
replies
619
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 4.1 years ago by
Michael Love
36k • written 4.1 years ago by
JP Carter
▴ 40
0
votes
2
replies
531
views
BAM file into R from Illumina
bam file
STAR
Illumina
updated 4.1 years ago by
ta_awwad
▴ 10 • written 4.1 years ago by
soheilazareie
• 0
0
votes
3
replies
1.1k
views
Error and warning message when reading the ballgown object
software error
illumina
DEG
ballgown
tuxedo
updated 4.1 years ago by
James W. MacDonald
59k • written 4.1 years ago by
amy16
• 0
1
vote
1
reply
719
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 4.5 years ago by
k.vitting.seerup
▴ 100 • written 4.5 years ago by
amy16
• 0
0
votes
3
replies
1.1k
views
How can I pre-process illumina raw file
illumina
microarray
updated 4.8 years ago by
James W. MacDonald
59k • written 4.8 years ago by
Agaz Hussain Wani
▴ 260
1
vote
3
replies
921
views
Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
4.9 years ago • updated 4.8 years ago
ezrabekele17
• 0
0
votes
0
replies
604
views
minfi error with dmpfinder
methylation
illumina
5.0 years ago
indranipoddar
• 0
0
votes
2
replies
1.1k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 5.0 years ago by
Guido Hooiveld
★ 3.2k • written 5.0 years ago by
Ellen O
• 0
0
votes
0
replies
1.6k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi
illumina
normalization
beadarray
5.0 years ago
hkarakurt
▴ 20
2
votes
1
reply
962
views
Differential Expression Analysis
differential gene expression
microarray
lumi
illumina
updated 5.2 years ago by
James W. MacDonald
59k • written 5.2 years ago by
paul.elliot1994
• 0
2
votes
3
replies
1.8k
views
Normalization of Illumina Microarray Data
illumina
microarray
normalization
updated 5.2 years ago by
Gordon Smyth
45k • written 5.2 years ago by
paul.elliot1994
• 0
0
votes
3
replies
947
views
MINFI missing samples in qcreports and densityplots
minfi
illumina
methylationEPIC
densityplot
5.4 years ago
annabelle.congras
▴ 10
0
votes
1
reply
723
views
Problems in using lumi for importing illumina raw data
beadarray
lumi
normalization
microarray
illumina
updated 5.4 years ago by
Gordon Smyth
45k • written 5.4 years ago by
Biologist
▴ 90
0
votes
4
replies
1.2k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db
aclust
methylation
annotation
illumina
updated 5.7 years ago by
b2cemaillist
• 0 • written 5.8 years ago by
aagata.szymanek
• 0
0
votes
0
replies
957
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads
methylation
illumina
epic microarray
5.7 years ago
rasii
• 0
2
votes
3
replies
1.1k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 5.7 years ago by
Gordon Smyth
45k • written 5.7 years ago by
Stane
▴ 40
0
votes
0
replies
774
views
Illumina Genotyping in parallel raise an error
crlmm
snp
illumina
5.9 years ago
nadne
▴ 10
6
votes
9
replies
977
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 5.9 years ago by
Gordon Smyth
45k • written 5.9 years ago by
Konstantinos Yeles
▴ 70
0
votes
1
reply
1.4k
views
Question about neqc and GEO illumina files
neqc
illumina
geo
limma
updated 5.9 years ago by
Gordon Smyth
45k • written 5.9 years ago by
akridgerunner
▴ 30
0
votes
2
replies
693
views
permutation with plink
illumina
plink
permutation
updated 6.0 years ago by
James W. MacDonald
59k • written 6.0 years ago by
sedrinne
• 0
0
votes
0
replies
622
views
Lumi Control Data
lumi
illumina
microarray
6.0 years ago
m.a.bentley
• 0
1
vote
14
replies
2.5k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools
qualitycontrol
HumanOmni5-4BeadChip
GenomeStudio
illumina
updated 6.0 years ago by
Stephanie M. Gogarten
▴ 820 • written 6.0 years ago by
Lna
• 0
0
votes
1
reply
753
views
Lumi error in importMethylIDAT
lumi
methylation
illumina
updated 6.0 years ago by
James W. MacDonald
59k • written 6.0 years ago by
rasii
• 0
0
votes
1
reply
1.1k
views
Error in Matrix
minfi
methylation
EPIC microarray
illumina
updated 6.1 years ago by
Kasper Daniel Hansen
6.5k • written 6.1 years ago by
rasii
• 0
3
votes
15
replies
3.3k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
6.1 years ago
rasii
• 0
0
votes
4
replies
965
views
minfi sample limit
minfi
illumina
illimina 450k methylation
methylation
updated 6.2 years ago by
Kasper Daniel Hansen
6.5k • written 6.2 years ago by
igor
▴ 40
0
votes
3
replies
1.3k
views
neqc normalization results in bimodal histogram of expression values
neqc
limma
microarray
illumina
updated 6.2 years ago by
Gordon Smyth
45k • written 6.2 years ago by
alexvpickering
▴ 110
0
votes
2
replies
913
views
clustering analysis of illumina microarray gene expression data
clustering
illumina
microarray
6.2 years ago
kritikamish99
▴ 10
4
votes
8
replies
6.2k
views
how to use idat file for analyses in bioconductor
microarray
illumina
idat
updated 6.3 years ago by
Gordon Smyth
45k • written 6.3 years ago by
kritikamish99
▴ 10
0
votes
0
replies
959
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina
450k
ChAMP
paired test
6.3 years ago
walter_teng
• 0
7
votes
4
replies
1.0k
views
very high adjusted P-vals using Illumina data from GEO
limma
p values
microarray
illumina
updated 6.3 years ago by
James W. MacDonald
59k • written 6.3 years ago by
Jason
▴ 20
0
votes
0
replies
906
views
Repetitive motifs on Illumina 450k derived sequences
illumina
450k
motifs
meme
6.3 years ago
Gustavo Fernández Bayón
▴ 440
0
votes
0
replies
641
views
Problems using the savR package
savR
illumina
6.4 years ago
merella.stefania
• 0
2
votes
1
reply
1.0k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina
bioconductor
limma
microarray
normalization
updated 6.5 years ago by
Gordon Smyth
45k • written 6.5 years ago by
Konstantinos Yeles
▴ 70
1
vote
6
replies
1.4k
views
Copy number analysis from Illumina 550K chip
illumina
copynumber
crlmm
6.6 years ago
stuti.agrawal
• 0
1
vote
1
reply
852
views
Error genotyping with CRLMM
crlmm
copynumber
illumina
updated 6.6 years ago by
andrew.j.skelton73
▴ 360 • written 6.6 years ago by
stuti.agrawal
• 0
0
votes
4
replies
1.7k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina
annotation
updated 6.6 years ago by
Mike Smith
★ 5.5k • written 6.6 years ago by
kanacska
▴ 10
0
votes
2
replies
1.3k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray
illumina
methylation
microarray
updated 6.6 years ago by
Sean Davis
21k • written 6.6 years ago by
maria.keays
• 0
11
votes
5
replies
1.6k
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 6.7 years ago by
Mark Cowley
▴ 400 • written 6.7 years ago by
willj
▴ 30
50 results • Page
1 of 1
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Replies
Comment: Handling of missing values in limma
by
AyHi
• 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files
by
lesefo6448
• 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
Comment: featureCounts: 0% successfully assigned fragments
by
ATpoint
★ 1.2k
What you have to do is to check whether the chromosome names in the BAM file are part of the GTF. Do it programatically, not by eye. Extrac…
Comment: champ.SVD() error, assumes standard class() function will return single string
by
Basti
▴ 280
What is class(`yourbeta`) ?
Answer: methylated/unmethylated media threshold (EPIC assay)
by
ramonfallon
• 0
OK, so the closest I could get as an answer to this was from a Kasper Hansen Illumina video from 2013 Where he says there have been some d…
Votes
Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
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