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frma
•
reset
0
votes
2
replies
493
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy
rma
frma
oligo
updated 2.5 years ago by
James W. MacDonald
59k • written 2.5 years ago by
chziy429
• 0
4
votes
5
replies
770
views
fRMA results different for Windows and Linux
frma
expr
gene expression data
affy
updated 4.0 years ago by
James W. MacDonald
59k • written 4.0 years ago by
osieman52
• 0
0
votes
2
replies
508
views
HG-U219 vectors for fRMA?
frma
frmatools
updated 4.1 years ago by
Matthew McCall
▴ 830 • written 4.1 years ago by
skol
• 0
2
votes
3
replies
1.6k
views
hgu133plus2hsentrezgcdf or hgu133ahsentrezgcdf packages not installing
readaffy
frma
affy
package installation
hgu133a
4.2 years ago
Chris Mancuso
• 0
0
votes
5
replies
886
views
How to normalize mouse gene 1.0st arry using frma?
microarray
frma
updated 4.2 years ago by
emacreamoinn
• 0 • written 5.0 years ago by
aritra
• 0
3
votes
1
reply
865
views
Processing several GSM from GEO database using Barcode and fRMA
frma
barcode
geneexpression
gsm
ncbi geo
updated 4.5 years ago by
Matthew McCall
▴ 830 • written 4.5 years ago by
diana.elassal
• 0
0
votes
3
replies
752
views
fRMA normalization for Mouse Gene 2.1 ST Array
frma
affymetrix mouse gene arrays
updated 5.0 years ago by
Matthew McCall
▴ 830 • written 5.0 years ago by
arisarkar88
• 0
3
votes
9
replies
1.1k
views
About the best use of frma for several GEO Series
frma
normalization
preprocessing
updated 5.4 years ago by
Matthew McCall
▴ 830 • written 5.4 years ago by
ctruntzer
▴ 20
1
vote
4
replies
719
views
Summarization probe ID to gene : FRMA
summarization
FRMA
affy
updated 5.6 years ago by
James W. MacDonald
59k • written 5.6 years ago by
Shamim Sarhadi
▴ 20
0
votes
4
replies
1.1k
views
fRMA error - unable to create unique mapping
frma
frmatools
affy
updated 5.6 years ago by
Matthew McCall
▴ 830 • written 5.6 years ago by
yesitsjess
• 0
0
votes
0
replies
792
views
In the frmaTools package, how can I makeVectorsFeatureSet() output include probeVecCore like the pre-built vectors?
frma
frmatools
affymetrix microarrays
6.2 years ago
jperezrogers
• 0
2
votes
5
replies
1.2k
views
fRMA: Applying mouse4302frmavecs on HT_MG-430_PM Arrays
frma
microarray
affiymetrix
6.3 years ago
Matthias Z.
▴ 20
0
votes
3
replies
993
views
frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
frma
affymetrix
barcode
updated 6.3 years ago by
Matthew McCall
▴ 830 • written 6.3 years ago by
minnie
• 0
7
votes
6
replies
4.6k
views
How to use brainarray custom cdf with oligo package?
oligo
customcdf
HTA
frma
updated 6.7 years ago by
James W. MacDonald
59k • written 6.7 years ago by
sanj
▴ 20
1
vote
3
replies
1.0k
views
Problem with frma median_polish
software error
frma
updated 6.7 years ago by
Matthew McCall
▴ 830 • written 6.7 years ago by
Thomas Pfau
▴ 20
1
vote
5
replies
1.2k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma
bioconductor
batcheffect
Primeview
insilicomerging
updated 7.1 years ago by
Matthew McCall
▴ 830 • written 7.1 years ago by
svlachavas
▴ 780
2
votes
2
replies
952
views
Strategies for fRMA on custom dataset(s)?
frma
frmatools
updated 7.3 years ago by
Matthew McCall
▴ 830 • written 7.3 years ago by
Ryan C. Thompson
7.8k
2
votes
8
replies
1.6k
views
frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?
frma
frmatools
updated 7.3 years ago by
Matthew McCall
▴ 830 • written 7.3 years ago by
Ryan C. Thompson
7.8k
0
votes
2
replies
845
views
How many arrays are "enough" for creating useful fRMA vectors?
annotation
frma
frmatools
updated 7.4 years ago by
Matthew McCall
▴ 830 • written 7.4 years ago by
Tim Triche
★ 4.2k
0
votes
2
replies
1.1k
views
barcode support for other platforms
frma
updated 7.7 years ago by
Matthew McCall
▴ 830 • written 7.7 years ago by
Guest User
★ 12k
0
votes
5
replies
1.3k
views
Single sample normalization of single-channel Agilent microarrays
affy
frma
SCAN.UPC
affy
frma
SCAN.UPC
updated 7.7 years ago by
Ryan C. Thompson
7.8k • written 7.7 years ago by
Guest User
★ 12k
0
votes
9
replies
1.6k
views
frma and alternative CDFs
GO
cdf
frma
BRAIN
GO
cdf
frma
BRAIN
updated 7.8 years ago by
Matthew McCall
▴ 830 • written 7.8 years ago by
Guest User
★ 12k
0
votes
6
replies
2.3k
views
processing Illumina HT12v4.0 expression data from GEO
Normalization
affy
PROcess
GEOquery
frma
Normalization
affy
PROcess
GEOquery
frma
updated 7.8 years ago by
Sean Davis
21k • written 7.8 years ago by
Abhishek Pratap
▴ 170
0
votes
0
replies
807
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO
probe
PROcess
frma
GO
probe
PROcess
frma
7.9 years ago
Matthew McCall
▴ 830
0
votes
6
replies
2.2k
views
converting probeset id to gene id's : fRMA
probe
affy
convert
frma
probe
affy
convert
frma
updated 7.9 years ago by
Peter Langfelder
★ 2.6k • written 7.9 years ago by
Abhishek Pratap
▴ 170
0
votes
1
reply
1.1k
views
fRMA- more issues with custom CDFs
GO
probe
frma
GO
probe
frma
updated 8.1 years ago by
Matthew McCall
▴ 830 • written 8.1 years ago by
Cornwell, Adam
▴ 110
0
votes
1
reply
875
views
fRMA- more issues with custom CDFs
GO
probe
frma
GO
probe
frma
updated 8.3 years ago by
Matthew McCall
▴ 830 • written 8.3 years ago by
Cornwell, Adam
▴ 110
0
votes
1
reply
1.5k
views
fRMA for Gene ST arrays
Microarray
probe
oligo
frma
Microarray
probe
oligo
frma
updated 8.3 years ago by
Matthew McCall
▴ 830 • written 8.3 years ago by
maria
▴ 10
0
votes
9
replies
1.6k
views
using frma and brainarray cdf on exon arrays
cdf
affy
PROcess
oligo
xps
frma
cdf
affy
PROcess
oligo
xps
frma
updated 8.4 years ago by
Stephen Piccolo
▴ 580 • written 8.4 years ago by
Ty Thomson
▴ 100
0
votes
3
replies
746
views
Fwd: Annotation discrepancy
probe
frma
probe
frma
updated 8.4 years ago by
James W. MacDonald
59k • written 8.4 years ago by
Eric Zollars
▴ 30
0
votes
0
replies
893
views
Annotation discrepancy HT HGU 133+ PM chip
probe
frma
probe
frma
8.4 years ago
Eric Zollars
▴ 30
0
votes
1
reply
797
views
combination of frma, combat and barcode methods
frma
frma
updated 8.5 years ago by
Matthew McCall
▴ 830 • written 8.5 years ago by
Raquel Martinez Garcia
▴ 50
0
votes
5
replies
1.1k
views
SCAN.UPC for Illumina arrays?
RNASeq
qPCR
affy
oligo
frma
RNASeq
qPCR
affy
oligo
frma
updated 8.5 years ago by
Stephen Piccolo
▴ 580 • written 8.5 years ago by
Tim Triche
★ 4.2k
0
votes
2
replies
3.6k
views
Normalization before ComBat
Microarray
Normalization
probe
affy
frma
Microarray
Normalization
probe
affy
frma
updated 8.6 years ago by
francesco.brundu@gmail.com
▴ 40 • written 8.6 years ago by
W. Evan Johnson
▴ 840
0
votes
2
replies
720
views
looking for data file for ATH1 (GPL198)
PROcess
frma
PROcess
frma
updated 8.6 years ago by
Loraine, Ann
▴ 50 • written 8.6 years ago by
Matthew McCall
▴ 830
0
votes
2
replies
1.1k
views
frma normalization and batch effects
Normalization
frma
Normalization
frma
updated 8.7 years ago by
Wolfgang Huber
13k • written 8.7 years ago by
Guest User
★ 12k
0
votes
0
replies
746
views
回复: Re: fRMA package
affxparser
frma
GenomicRanges
affxparser
frma
GenomicRanges
8.8 years ago
Hanyine
▴ 30
0
votes
0
replies
1.0k
views
FW: fRMA package
affxparser
frma
GenomicRanges
affxparser
frma
GenomicRanges
8.8 years ago
Li Liu
▴ 100
0
votes
1
reply
820
views
frmaTools library error :: makeVectorsAffyBatch() function
Microarray
probe
frma
frmaTools
Microarray
probe
frma
frmaTools
updated 9.0 years ago by
Matthew McCall
▴ 830 • written 9.0 years ago by
Tae-Hoon Chung
▴ 70
0
votes
1
reply
782
views
fRMA without using ReadAffy()
frma
SCAN.UPC
frma
SCAN.UPC
updated 9.0 years ago by
Matthew McCall
▴ 830 • written 9.0 years ago by
S.D. Chorlton
▴ 10
0
votes
0
replies
684
views
Normalizing a dataset from GEO to suit a classifier trained on another dataset
Microarray
Normalization
Preprocessing
probe
affy
preprocessCore
frma
Microarray
probe
9.1 years ago
Matthew McCall
▴ 830
0
votes
1
reply
776
views
fRMA for Gene ST arrays
affy
oligo
frma
ASSIGN
affy
oligo
frma
ASSIGN
updated 9.1 years ago by
Matthew McCall
▴ 830 • written 9.1 years ago by
Kamila Naxerova
▴ 100
0
votes
6
replies
1.1k
views
barcode with custom CDF
cdf
frma
frmaTools
cdf
frma
frmaTools
updated 9.2 years ago by
Stephen Piccolo
▴ 580 • written 9.2 years ago by
Guest User
★ 12k
0
votes
3
replies
1.2k
views
Using fRMA with "alternative" CDF files
Normalization
cdf
frma
Normalization
cdf
frma
updated 9.3 years ago by
Matthew McCall
▴ 830 • written 9.4 years ago by
Cornwell, Adam
▴ 110
0
votes
2
replies
1.0k
views
frma for Nimblegen arrays?
Microarray
Annotation
Normalization
affy
PROcess
safe
frma
frmaTools
Microarray
affy
updated 9.5 years ago by
Benilton Carvalho
★ 4.3k • written 9.5 years ago by
wrighth
▴ 260
0
votes
0
replies
812
views
Issue with Genome Graphs
Annotation
simpleaffy
oligo
GenomeGraphs
frma
Annotation
simpleaffy
oligo
GenomeGraphs
9.5 years ago
Jeremy Ng
▴ 180
0
votes
1
reply
812
views
[combat] UPC availablility
affy
frma
SCAN.UPC
affy
frma
SCAN.UPC
updated 9.5 years ago by
Stephen Piccolo
▴ 580 • written 9.5 years ago by
W. Evan Johnson
▴ 840
0
votes
5
replies
958
views
frma for Nimblegen arrays?
Microarray
Normalization
affy
PROcess
safe
frma
Microarray
Normalization
affy
PROcess
updated 9.6 years ago by
Matthew McCall
▴ 830 • written 9.6 years ago by
wrighth
▴ 260
0
votes
2
replies
864
views
New Bioconductor Package: SCAN.UPC
Normalization
affy
frma
Normalization
affy
frma
updated 9.6 years ago by
Stephen Piccolo
▴ 580 • written 9.6 years ago by
W. Evan Johnson
▴ 840
0
votes
0
replies
2.2k
views
Seperate quantile normalization but common probe summary by median polish (oligo package)?
Normalization
probe
oligo
frma
frmaTools
Normalization
probe
oligo
frma
frmaTools
9.8 years ago
Schott, Johanna
▴ 20
50 results • Page
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• 0
Hi, That was helpful. Thank you. How to do the same for the testing data?
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After going through the package, I think all the peaks are annotated to genes irrespective of distance to TSS. There is also another functi…
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