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scan.upc
•
reset
1
vote
3
replies
1.6k
views
SCAN UPC normalisation
normalization
scan.upc
9.1 years ago
sanj
▴ 20
2
votes
8
replies
1.9k
views
Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
microarray
scan.upc
hta2.0
updated 6.3 years ago by
Stephen Piccolo
▴ 590 • written 6.4 years ago by
Lukas__
• 0
0
votes
1
reply
1.2k
views
[combat] UPC availablility
affy
frma
SCAN.UPC
affy
frma
SCAN.UPC
updated 11.5 years ago by
Stephen Piccolo
▴ 590 • written 11.5 years ago by
W. Evan Johnson
▴ 850
0
votes
1
reply
1.4k
views
SCAN-UPC: 12079 of 22283 probes returned for hgu133a CELs?
hgu133a
probe
affy
SCAN.UPC
hgu133a
probe
affy
SCAN.UPC
updated 11.2 years ago by
Andrew Yates
▴ 20 • written 11.2 years ago by
Stephen Piccolo
▴ 590
0
votes
1
reply
1.5k
views
SCAN-UPC: 12079 of 22283 probes returned for hgu133a CELs?
Normalization
hgu133a
probe
affy
PROcess
SCAN.UPC
Normalization
hgu133a
probe
affy
updated 11.0 years ago by
Andrew Yates
▴ 20 • written 11.0 years ago by
Stephen Piccolo
▴ 590
0
votes
1
reply
1.2k
views
fRMA without using ReadAffy()
frma
SCAN.UPC
frma
SCAN.UPC
updated 10.9 years ago by
Matthew McCall
▴ 830 • written 10.9 years ago by
S.D. Chorlton
▴ 10
0
votes
2
replies
1.5k
views
SCAN.UPC vs NUSE
affy
affyPLM
SCAN.UPC
affy
affyPLM
SCAN.UPC
updated 10.6 years ago by
Stephen Piccolo
▴ 590 • written 10.6 years ago by
Leif Peterson
▴ 10
0
votes
3
replies
1.3k
views
ParseMetaFromGtfFile is.na() error
Annotation
SCAN.UPC
Annotation
SCAN.UPC
updated 9.9 years ago by
Michael Lawrence
★ 11k • written 9.9 years ago by
Guest User
★ 13k
2
votes
4
replies
1.2k
views
SCAN.UPC : lost too many samples from GSE (BrainArray + ConvThreshold)
SCAN.UPC
probe
normalization
GEOdata
cancer
5.1 years ago
s.goncalvesclaro
▴ 10
0
votes
1
reply
1.4k
views
SCAN UPC probability - validation of gene expression results using UPC
hgu133a2
safe
SCAN.UPC
hgu133a2
safe
SCAN.UPC
updated 11.5 years ago by
Stephen Piccolo
▴ 590 • written 11.5 years ago by
W. Evan Johnson
▴ 850
0
votes
3
replies
1.5k
views
SCAN.UPC giving error for multiple input files
scan.upc
updated 8.7 years ago by
Stephen Piccolo
▴ 590 • written 8.7 years ago by
Vani
▴ 20
0
votes
1
reply
1.2k
views
SCAN.UPC eset not providing phenoData
scan.upc
eset
updated 8.7 years ago by
Stephen Piccolo
▴ 590 • written 8.7 years ago by
Jo
▴ 30
0
votes
1
reply
1.2k
views
RNA-Seq Read Counts for SCAN.UPC
scan.upc
rnaseq
updated 8.4 years ago by
Stephen Piccolo
▴ 590 • written 8.4 years ago by
Jo
▴ 30
0
votes
1
reply
1.2k
views
UPC RNA-Seq individual samples
scan.upc
upc
rnaseq
updated 8.4 years ago by
Stephen Piccolo
▴ 590 • written 8.4 years ago by
Jo
▴ 30
0
votes
2
replies
1.5k
views
UPC method giving error for Microarray dataset
scan.upc
UPC
updated 8.4 years ago by
Stephen Piccolo
▴ 590 • written 8.4 years ago by
Vani
▴ 20
0
votes
2
replies
1.4k
views
UPC correction for GC content?
scan.upc
upc_generic_expressionset
upc
updated 8.2 years ago by
Stephen Piccolo
▴ 590 • written 8.2 years ago by
minnie
• 0
1
vote
2
replies
1.1k
views
UPC transposes output data
scan.upc
updated 7.2 years ago by
Stephen Piccolo
▴ 590 • written 7.2 years ago by
guus.steeg
▴ 10
4
votes
13
replies
2.1k
views
Why is batch effect correction an option in SCAN.UPC normalization?
scan.upc
upc
normalization
batch effect correction
updated 5.7 years ago by
Stephen Piccolo
▴ 590 • written 5.7 years ago by
y.li.1
• 0
1
vote
4
replies
1.2k
views
ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
annotation
SCAN.UPC
updated 6.7 years ago by
Stephen Piccolo
▴ 590 • written 6.7 years ago by
lhuang7
▴ 50
0
votes
5
replies
1.9k
views
Single sample normalization of single-channel Agilent microarrays
affy
frma
SCAN.UPC
affy
frma
SCAN.UPC
updated 9.7 years ago by
Ryan C. Thompson
★ 7.9k • written 9.7 years ago by
Guest User
★ 13k
2
votes
13
replies
2.8k
views
SCAN.UPC: exception thrown when loading GEOQuery
scan.upc
geoquery
rcurl
9.3 years ago
lep
▴ 90
0
votes
1
reply
1.2k
views
SCAN.UPC for Agilent single channel and Illumina
microarray
scan.upc
updated 9.2 years ago by
Stephen Piccolo
▴ 590 • written 9.2 years ago by
sathyabaarathi
• 0
0
votes
4
replies
1.7k
views
SCAN-normalized values on log2 scale?
scan.upc
updated 8.8 years ago by
Stephen Piccolo
▴ 590 • written 8.8 years ago by
Jenny Drnevich
★ 2.0k
0
votes
0
replies
885
views
FYI: SCAN.UPC and HuGene 1/2 arrays
SCAN.UPC
SCAN.UPC
9.9 years ago
Stephen Piccolo
▴ 590
0
votes
0
replies
1.1k
views
about expression value generated by SCAN UPC package
SCAN.UPC
SCAN.UPC
11.1 years ago
gregory voisin
▴ 430
0
votes
3
replies
1.2k
views
Comparing SCAN Q.value with Meta-Analyses Q.Value
scan.upc
scan
meta
q value
8.4 years ago
Jo
▴ 30
1
vote
3
replies
1.2k
views
Normalization of multiple HTA 2.0 arays using SCAN.UPC
scan.upc
6.5 years ago
Seymoo
• 0
0
votes
0
replies
1.2k
views
Problem when trying to use \'affy\' package
Normalization
GO
affy
sva
SCAN.UPC
Normalization
GO
affy
sva
SCAN.UPC
10.3 years ago
Kaj Chokeshaiusaha
▴ 140
1
vote
2
replies
1.4k
views
Problem Installing SCAN.UPC
scan.upc
installation
bioconductor
8.8 years ago
Vani
▴ 20
0
votes
9
replies
2.3k
views
Question about Agilent microarray data measurement
Agilent
limma
scan.upc
microarray
7.5 years ago
Maximilian
▴ 10
0
votes
1
reply
998
views
Error when using write.table() with SCAN.UPC ESET
scan.upc
write.table
8.8 years ago
Vani
▴ 20
0
votes
1
reply
1.2k
views
Error with SCAN.UPC UPC_RNASeq method
scan.upc
RNA-Seq
UPC
8.4 years ago
vn
• 0
32 results • Page
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Recent ...
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Thank you Tim, this is a great help in getting me started!
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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…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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
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