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illuminaio
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5
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5
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Normalization of IDAT files from Illumina HumanMethylation450 BeadChip without .bgx file
IlluminaHumanMethylation450BeadChip
illuminaio
normalize450K
2.1 years ago • updated 2.0 years ago
Sarah
• 0
2
votes
4
replies
1.3k
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis
illuminaio
beadarray
DSS
bsseqData
2.2 years ago
Jojo
• 0
3
votes
9
replies
5.7k
views
Illumina Expression analysis from iDAT files
beadarray
lumi
illuminaio
idat
updated 2.4 years ago by
Gordon Smyth
50k • written 10.4 years ago by
Sean Davis
21k
1
vote
2
replies
1.1k
views
read.idat and empty Symbols
illuminaio
limma
7.4 years ago • updated 3.5 years ago
h.mon
• 0
0
votes
2
replies
1.0k
views
Question about Illuminaio
illuminaio
illumina human ht-12 v4
gene expression
micorarray
updated 6.1 years ago by
Mike Smith
★ 6.5k • written 6.1 years ago by
makoouji
• 0
0
votes
2
replies
1.3k
views
IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
illuminaio
illuminahumanmethylationepicmanifest
minfi
updated 6.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 6.3 years ago by
Giovanni Calice
▴ 160
0
votes
1
reply
1.8k
views
bug limma / illuminaio? Otherwise small feature request...
limma
illuminaio
idat
gzip
updated 7.0 years ago by
Matthew Ritchie
▴ 1000 • written 7.0 years ago by
Guido Hooiveld
★ 3.9k
1
vote
5
replies
2.9k
views
Error with read.idat() function in illuminaio package
illuminaio
normalization
updated 7.0 years ago by
Matthew Ritchie
▴ 1000 • written 8.8 years ago by
Stephen Piccolo
▴ 590
1
vote
2
replies
1.6k
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi
illuminaio
epic
7.8 years ago
m.van_iterson
▴ 20
1
vote
2
replies
2.0k
views
Further analysis of methylation microarrays data (Illumina - idat) after reading by illuminaio package
limma
lumi
illuminaio
illimina 450k methylation
microarray
8.1 years ago
Adam
• 0
4
votes
10
replies
2.2k
views
Zero values for bead backgrounds (reading idat files using Illuminaio)
illuminaio
idat
beadarray
updated 8.6 years ago by
Mike Smith
★ 6.5k • written 8.7 years ago by
willj
▴ 30
1
vote
4
replies
2.6k
views
read.idat manifest error
limma
illuminaio
illumina human WG6v2
updated 8.9 years ago by
Matthew Ritchie
▴ 1000 • written 8.9 years ago by
Gabriel Nathan Kaufman, Mr
▴ 60
0
votes
10
replies
2.2k
views
Error when using readIDAT() from illuminaio
illuminaio
idat
9.2 years ago
lacion
• 0
0
votes
1
reply
2.3k
views
Reading IDAT files with illuminaio
SNP
illuminaio
SNP
illuminaio
updated 10.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.4 years ago by
Mike Smith
★ 6.5k
0
votes
0
replies
1.8k
views
Illumina Expression analysis from iDAT files
Normalization
limma
beadarray
lumi
illuminaio
Normalization
limma
beadarray
lumi
10.4 years ago
Kasper Daniel Hansen
★ 6.5k
15 results • Page
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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