Showing : Illumina • reset
0
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5
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2.2k
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Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
written 8.8 years ago by • 0
1
vote
4
replies
1.3k
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
15 months ago mikat • 0
1
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1
reply
1.7k
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 2.5 years ago by ★ 4.0k • written 2.5 years ago by • 0
0
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0
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1.4k
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Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
3.1 years ago octaviompa • 0
0
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2
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1.2k
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4.3 years ago sissialva21 • 0
2
votes
4
replies
2.1k
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 4.4 years ago by 52k • written 4.4 years ago by • 0
1
vote
3
replies
1.9k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
5.3 years ago erwin.tomasich ▴ 10
0
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7
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2.6k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 6.0 years ago by ★ 4.1k • written 6.0 years ago by • 0
1
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2
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1.7k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 6.4 years ago by ★ 1.3k • written 6.4 years ago by • 0
1
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4
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2.4k
views
Trouble loading 'lumi' package
lumi illumina hdf5array
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 30
2
votes
5
replies
3.0k
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 3.4 years ago by ▴ 10 • written 6.9 years ago by • 0
2
votes
4
replies
1.7k
views
The error when using beadarry and limma packages for analysing illumina chip
limma beadarray illumina
updated 7.0 years ago by 52k • written 7.0 years ago by ▴ 10
1
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1
reply
2.2k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 10
1
vote
1
reply
1.9k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm gsa microarray illumina
written 7.1 years ago by • 0
1
vote
5
replies
1.5k
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 7.1 years ago by 43k • written 7.1 years ago by ▴ 40
0
votes
2
replies
1.4k
views
BAM file into R from Illumina
bam file STAR Illumina
updated 7.1 years ago by ▴ 10 • written 7.1 years ago by • 0
0
votes
3
replies
2.2k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
1
vote
1
reply
1.7k
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 7.5 years ago by ▴ 120 • written 7.5 years ago by • 0
0
votes
3
replies
1.8k
views
How can I pre-process illumina raw file
illumina microarray
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 260
1
vote
3
replies
1.8k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
7.9 years ago ezrabekele17 • 0
0
votes
0
replies
1.1k
views
minfi error with dmpfinder
methylation illumina
8.0 years ago indranipoddar • 0
0
votes
2
replies
2.7k
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 8.0 years ago by ★ 4.1k • written 8.0 years ago by • 0
0
votes
0
replies
2.8k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi illumina normalization beadarray
8.0 years ago hkarakurt ▴ 20
2
votes
1
reply
1.8k
views
Differential Expression Analysis
differential gene expression microarray lumi illumina
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
2
votes
3
replies
3.0k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 8.2 years ago by 52k • written 8.2 years ago by • 0
0
votes
3
replies
2.0k
views
MINFI missing samples in qcreports and densityplots
minfi illumina methylationEPIC densityplot
8.4 years ago annabelle.congras ▴ 10
0
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1
reply
1.7k
views
Problems in using lumi for importing illumina raw data
beadarray lumi normalization microarray illumina
updated 8.4 years ago by 52k • written 8.4 years ago by ▴ 120
0
votes
0
replies
1.8k
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads methylation illumina epic microarray
8.7 years ago rasii • 0
2
votes
3
replies
1.8k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 8.7 years ago by 52k • written 8.7 years ago by ▴ 40
0
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0
replies
1.4k
views
Illumina Genotyping in parallel raise an error
crlmm snp illumina
8.9 years ago nadne ▴ 10
6
votes
9
replies
2.0k
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 8.9 years ago by 52k • written 8.9 years ago by ▴ 80
0
votes
1
reply
2.5k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 8.9 years ago by 52k • written 8.9 years ago by ▴ 30
0
votes
2
replies
1.5k
views
permutation with plink
illumina plink permutation
updated 9.0 years ago by 68k • written 9.0 years ago by • 0
0
votes
0
replies
1.2k
views
Lumi Control Data
lumi illumina microarray
9.0 years ago m.a.bentley • 0
3
votes
14
replies
4.6k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 9.0 years ago by ▴ 890 • written 9.0 years ago by • 0
0
votes
1
reply
1.4k
views
Lumi error in importMethylIDAT
lumi methylation illumina
updated 9.1 years ago by 68k • written 9.1 years ago by • 0
0
votes
1
reply
1.9k
views
Error in Matrix
minfi methylation EPIC microarray illumina
updated 9.1 years ago by ★ 6.5k • written 9.1 years ago by • 0
3
votes
15
replies
5.3k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
9.1 years ago rasii • 0
0
votes
4
replies
1.9k
views
minfi sample limit
minfi illumina illimina 450k methylation methylation
updated 9.2 years ago by ★ 6.5k • written 9.2 years ago by ▴ 50
0
votes
3
replies
2.6k
views
neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 9.2 years ago by 52k • written 9.2 years ago by ▴ 110
0
votes
2
replies
1.6k
views
clustering analysis of illumina microarray gene expression data
clustering illumina microarray
9.3 years ago • updated 9.2 years ago kritikamish99 ▴ 10
4
votes
8
replies
12k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 9.3 years ago by 52k • written 9.3 years ago by ▴ 10
0
votes
0
replies
1.6k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina 450k ChAMP paired test
9.3 years ago walter_teng • 0
7
votes
4
replies
2.0k
views
very high adjusted P-vals using Illumina data from GEO
limma p values microarray illumina
updated 9.3 years ago by 68k • written 9.3 years ago by ▴ 20
0
votes
0
replies
1.5k
views
Repetitive motifs on Illumina 450k derived sequences
illumina 450k motifs meme
9.3 years ago Gustavo Fernández Bayón ▴ 440
0
votes
0
replies
1.1k
views
Problems using the savR package
savR illumina
9.4 years ago merella.stefania • 0
2
votes
1
reply
1.8k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina bioconductor limma microarray normalization
updated 9.5 years ago by 52k • written 9.5 years ago by ▴ 80
1
vote
6
replies
2.6k
views
Copy number analysis from Illumina 550K chip
illumina copynumber crlmm
9.6 years ago stuti.agrawal • 0
1
vote
1
reply
1.6k
views
Error genotyping with CRLMM
crlmm copynumber illumina
updated 9.6 years ago by ▴ 370 • written 9.6 years ago by • 0
0
votes
4
replies
2.9k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina annotation
updated 9.6 years ago by ★ 6.6k • written 9.6 years ago by ▴ 10
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Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
``` library(org.Dm.eg.db) rn <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "SYMBOL","FLYBASE") ## ensure no NA values get propaga…
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your explanation, that makes sense. Do you have any suggestions on how to deal with this issue? if it is an issue? especially…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by nytwordlehints • 0
I have always had a great fondness for games, so witnessing their transformation into animated versions is truly a delightful experience. […
Comment: FlowSOM is unable to create Output by EvangelinePope • 0
I will remember it, Thank you so much for sharing.
Answer: Limma suqeezeVar by Gordon Smyth 52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
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Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
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