Showing : illumina • reset
1
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4
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610
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
4 months ago mikat • 0
1
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1
reply
1.0k
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 19 months ago by ★ 3.9k • written 19 months ago by • 0
0
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0
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973
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Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.2 years ago octaviompa • 0
0
votes
2
replies
900
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
3.4 years ago sissialva21 • 0
2
votes
4
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1.7k
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 3.5 years ago by 51k • written 3.5 years ago by • 0
1
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3
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1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.4 years ago erwin.tomasich ▴ 10
0
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7
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2.1k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
1
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2
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1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 5.5 years ago by ★ 1.3k • written 5.5 years ago by • 0
1
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4
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1.9k
views
Trouble loading 'lumi' package
lumi illumina hdf5array
updated 5.8 years ago by 66k • written 5.8 years ago by ▴ 30
2
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5
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2.4k
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 2.5 years ago by ▴ 10 • written 6.0 years ago by • 0
2
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4
replies
1.4k
views
The error when using beadarry and limma packages for analysing illumina chip
limma beadarray illumina
updated 6.0 years ago by 51k • written 6.0 years ago by ▴ 10
1
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1
reply
1.8k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 6.1 years ago by 66k • written 6.1 years ago by ▴ 10
1
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1
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1.5k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm gsa microarray illumina
written 6.1 years ago by • 0
1
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5
replies
1.2k
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 6.1 years ago by 42k • written 6.1 years ago by ▴ 40
0
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2
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1.1k
views
BAM file into R from Illumina
bam file STAR Illumina
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by • 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.2 years ago by 66k • written 6.2 years ago by • 0
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 6.6 years ago by ▴ 120 • written 6.6 years ago by • 0
0
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3
replies
1.5k
views
How can I pre-process illumina raw file
illumina microarray
updated 6.9 years ago by 66k • written 6.9 years ago by ▴ 260
1
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3
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1.5k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
6.9 years ago ezrabekele17 • 0
0
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0
replies
983
views
minfi error with dmpfinder
methylation illumina
7.1 years ago indranipoddar • 0
0
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2
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1.9k
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 7.1 years ago by ★ 4.0k • written 7.1 years ago by • 0
0
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0
replies
2.5k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi illumina normalization beadarray
7.1 years ago hkarakurt ▴ 20
2
votes
1
reply
1.5k
views
Differential Expression Analysis
differential gene expression microarray lumi illumina
updated 7.3 years ago by 66k • written 7.3 years ago by • 0
2
votes
3
replies
2.5k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 7.3 years ago by 51k • written 7.3 years ago by • 0
0
votes
3
replies
1.7k
views
MINFI missing samples in qcreports and densityplots
minfi illumina methylationEPIC densityplot
7.4 years ago annabelle.congras ▴ 10
0
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1
reply
1.4k
views
Problems in using lumi for importing illumina raw data
beadarray lumi normalization microarray illumina
updated 7.5 years ago by 51k • written 7.5 years ago by ▴ 110
0
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4
replies
1.9k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
updated 7.7 years ago by • 0 • written 7.9 years ago by • 0
0
votes
0
replies
1.5k
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads methylation illumina epic microarray
7.8 years ago rasii • 0
2
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3
replies
1.6k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 7.8 years ago by 51k • written 7.8 years ago by ▴ 40
0
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0
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1.1k
views
Illumina Genotyping in parallel raise an error
crlmm snp illumina
8.0 years ago nadne ▴ 10
6
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9
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1.6k
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 8.0 years ago by 51k • written 8.0 years ago by ▴ 80
0
votes
1
reply
2.1k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 8.0 years ago by 51k • written 8.0 years ago by ▴ 30
0
votes
2
replies
1.2k
views
permutation with plink
illumina plink permutation
updated 8.1 years ago by 66k • written 8.1 years ago by • 0
0
votes
0
replies
1.0k
views
Lumi Control Data
lumi illumina microarray
8.1 years ago m.a.bentley • 0
1
vote
14
replies
3.8k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 8.1 years ago by ▴ 870 • written 8.1 years ago by • 0
0
votes
1
reply
1.2k
views
Lumi error in importMethylIDAT
lumi methylation illumina
updated 8.1 years ago by 66k • written 8.1 years ago by • 0
0
votes
1
reply
1.6k
views
Error in Matrix
minfi methylation EPIC microarray illumina
updated 8.1 years ago by ★ 6.5k • written 8.2 years ago by • 0
3
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15
replies
4.5k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
8.2 years ago rasii • 0
0
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4
replies
1.6k
views
minfi sample limit
minfi illumina illimina 450k methylation methylation
updated 8.3 years ago by ★ 6.5k • written 8.3 years ago by ▴ 50
0
votes
3
replies
2.2k
views
neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 8.3 years ago by 51k • written 8.3 years ago by ▴ 110
0
votes
2
replies
1.3k
views
clustering analysis of illumina microarray gene expression data
clustering illumina microarray
8.3 years ago kritikamish99 ▴ 10
4
votes
8
replies
10k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 8.3 years ago by 51k • written 8.3 years ago by ▴ 10
0
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0
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1.4k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina 450k ChAMP paired test
8.3 years ago walter_teng • 0
7
votes
4
replies
1.6k
views
very high adjusted P-vals using Illumina data from GEO
limma p values microarray illumina
updated 8.4 years ago by 66k • written 8.4 years ago by ▴ 20
0
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0
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1.4k
views
Repetitive motifs on Illumina 450k derived sequences
illumina 450k motifs meme
8.4 years ago Gustavo Fernández Bayón ▴ 440
0
votes
0
replies
944
views
Problems using the savR package
savR illumina
8.4 years ago merella.stefania • 0
2
votes
1
reply
1.5k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina bioconductor limma microarray normalization
updated 8.6 years ago by 51k • written 8.6 years ago by ▴ 80
1
vote
6
replies
2.1k
views
Copy number analysis from Illumina 550K chip
illumina copynumber crlmm
8.7 years ago stuti.agrawal • 0
1
vote
1
reply
1.3k
views
Error genotyping with CRLMM
crlmm copynumber illumina
updated 8.7 years ago by ▴ 370 • written 8.7 years ago by • 0
0
votes
4
replies
2.4k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina annotation
updated 8.7 years ago by ★ 6.5k • written 8.7 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Awards • All
Popular Question to swbarnes2 ★ 1.4k
Popular Question to Stephanie M. Gogarten ▴ 870
Popular Question to Jonathan ▴ 10
Popular Question to Frederico Moraes Ferreira ▴ 100
Popular Question to richardallenfriedmanbrooklyn ▴ 20
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