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illuminaio
•
reset
4
votes
5
replies
213
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Normalization of IDAT files from Illumina HumanMethylation450 BeadChip without .bgx file
IlluminaHumanMethylation450BeadChip
illuminaio
normalize450K
5 weeks ago • updated 24 days ago
Sarah
• 0
2
votes
4
replies
217
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis
illuminaio
beadarray
DSS
bsseqData
3 months ago
Jojo
• 0
0
votes
2
replies
545
views
Question about Illuminaio
illuminaio
illumina human ht-12 v4
gene expression
micorarray
updated 4.2 years ago by
Mike Smith
★ 5.5k • written 4.2 years ago by
makoouji
• 0
0
votes
2
replies
710
views
IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
illuminaio
illuminahumanmethylationepicmanifest
minfi
updated 4.4 years ago by
Kasper Daniel Hansen
6.5k • written 4.4 years ago by
Giovanni Calice
▴ 160
0
votes
1
reply
1.3k
views
bug limma / illuminaio? Otherwise small feature request...
limma
illuminaio
idat
gzip
updated 5.0 years ago by
Matthew Ritchie
▴ 1000 • written 5.0 years ago by
Guido Hooiveld
★ 3.2k
1
vote
5
replies
1.9k
views
Error with read.idat() function in illuminaio package
illuminaio
normalization
updated 5.0 years ago by
Matthew Ritchie
▴ 1000 • written 6.8 years ago by
Stephen Piccolo
▴ 580
1
vote
2
replies
600
views
read.idat and empty Symbols
illuminaio
limma
5.5 years ago • updated 19 months ago
h.mon
• 0
1
vote
2
replies
985
views
Problem reading EPIC array data: different bead locations on different EPIC Chips
minfi
illuminaio
epic
5.9 years ago
m.van_iterson
▴ 20
1
vote
2
replies
1.5k
views
Further analysis of methylation microarrays data (Illumina - idat) after reading by illuminaio package
limma
lumi
illuminaio
illimina 450k methylation
microarray
6.1 years ago
Adam
• 0
4
votes
10
replies
1.3k
views
Zero values for bead backgrounds (reading idat files using Illuminaio)
illuminaio
idat
beadarray
updated 6.7 years ago by
Mike Smith
★ 5.5k • written 6.7 years ago by
willj
▴ 30
1
vote
4
replies
1.8k
views
read.idat manifest error
limma
illuminaio
illumina human WG6v2
updated 6.9 years ago by
Matthew Ritchie
▴ 1000 • written 6.9 years ago by
Gabriel Nathan Kaufman, Mr
▴ 60
0
votes
10
replies
1.4k
views
Error when using readIDAT() from illuminaio
illuminaio
idat
7.2 years ago
lacion
• 0
0
votes
1
reply
1.9k
views
Reading IDAT files with illuminaio
SNP
illuminaio
SNP
illuminaio
updated 8.4 years ago by
Kasper Daniel Hansen
6.5k • written 8.4 years ago by
Mike Smith
★ 5.5k
0
votes
0
replies
1.4k
views
Illumina Expression analysis from iDAT files
Normalization
limma
beadarray
lumi
illuminaio
Normalization
limma
beadarray
lumi
8.5 years ago
Kasper Daniel Hansen
6.5k
3
votes
9
replies
4.2k
views
Illumina Expression analysis from iDAT files
beadarray
lumi
illuminaio
idat
updated 5 months ago by
Gordon Smyth
45k • written 8.5 years ago by
Sean Davis
21k
15 results • Page
1 of 1
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Replies
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Yang Shi
• 0
Got that sir, thanks so much!
Comment: UniprotKB AC/ID to Entrez ID Conversion
by
Guido Hooiveld
★ 3.2k
No, no need to modify `up`. It somehow has to do with the R.BioC version; it works when using the latest versions (R-4.2.0/BioC-3.15), but…
Comment: UniprotKB AC/ID to Entrez ID Conversion
by
tom.kloter
• 0
Thanks a lot for your response! I tried the code in my script and got to the following result: ``` > up <- UniProt.ws(taxId=9606) > up "U…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Guido Hooiveld
★ 3.2k
Regarding the normalization method (SCAN); I have only used RMA for the reasons James explained in one of your other threads (https://suppo…
Answer: UniprotKB AC/ID to Entrez ID Conversion
by
Guido Hooiveld
★ 3.2k
The key to realize is that your input is a vector of Uniprot **ID**s (also known as 'entry names') . The central identifier in the Uniprot …
Votes
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
A: coefficient not estimable (limma warning)
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