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illuminaio
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5
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3.6k
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Normalization of IDAT files from Illumina HumanMethylation450 BeadChip without .bgx file
IlluminaHumanMethylation450BeadChip
illuminaio
normalize450K
3.6 years ago • updated 3.5 years ago
Sarah
• 0
2
votes
4
replies
2.0k
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis
illuminaio
beadarray
DSS
bsseqData
3.8 years ago
Jojo
• 0
0
votes
2
replies
1.4k
views
Question about Illuminaio
illuminaio
illumina human ht-12 v4
gene expression
micorarray
updated 7.6 years ago by
Mike Smith
★ 6.6k • written 7.6 years ago by
makoouji
• 0
0
votes
2
replies
1.8k
views
IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
illuminaio
illuminahumanmethylationepicmanifest
minfi
updated 7.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.8 years ago by
Giovanni Calice
▴ 160
0
votes
1
reply
2.1k
views
bug limma / illuminaio? Otherwise small feature request...
limma
illuminaio
idat
gzip
updated 8.5 years ago by
Matthew Ritchie
▴ 1000 • written 8.5 years ago by
Guido Hooiveld
★ 4.1k
1
vote
5
replies
3.5k
views
Error with read.idat() function in illuminaio package
illuminaio
normalization
updated 8.5 years ago by
Matthew Ritchie
▴ 1000 • written 10.3 years ago by
Stephen Piccolo
▴ 600
1
vote
2
replies
1.4k
views
read.idat and empty Symbols
illuminaio
limma
8.9 years ago • updated 5.0 years ago
h.mon
• 0
1
vote
2
replies
2.1k
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi
illuminaio
epic
9.4 years ago • updated 9.3 years ago
m.van_iterson
▴ 20
1
vote
2
replies
2.6k
views
Further analysis of methylation microarrays data (Illumina - idat) after reading by illuminaio package
limma
lumi
illuminaio
illimina 450k methylation
microarray
9.6 years ago
Adam
• 0
4
votes
10
replies
3.1k
views
Zero values for bead backgrounds (reading idat files using Illuminaio)
illuminaio
idat
beadarray
updated 10.2 years ago by
Mike Smith
★ 6.6k • written 10.2 years ago by
willj
▴ 30
1
vote
4
replies
3.1k
views
read.idat manifest error
limma
illuminaio
illumina human WG6v2
updated 10.4 years ago by
Matthew Ritchie
▴ 1000 • written 10.4 years ago by
Gabriel Nathan Kaufman, Mr
▴ 60
0
votes
10
replies
2.9k
views
Error when using readIDAT() from illuminaio
illuminaio
idat
10.7 years ago
lacion
• 0
0
votes
1
reply
2.6k
views
Reading IDAT files with illuminaio
SNP
illuminaio
SNP
illuminaio
updated 11.9 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.9 years ago by
Mike Smith
★ 6.6k
0
votes
0
replies
2.2k
views
Illumina Expression analysis from iDAT files
Normalization
limma
beadarray
lumi
illuminaio
Normalization
limma
beadarray
lumi
11.9 years ago
Kasper Daniel Hansen
★ 6.5k
3
votes
9
replies
7.3k
views
Illumina Expression analysis from iDAT files
beadarray
lumi
illuminaio
idat
updated 3.9 years ago by
Gordon Smyth
53k • written 12.0 years ago by
Sean Davis
21k
15 results • Page
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Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot
by
Kevin Blighe
★ 4.0k
Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
Answer: gene Set with high AUC score but no cells assigned to cell type
by
Kevin Blighe
★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction
by
Kevin Blighe
★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
Kevin Blighe
★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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