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Showing :
frma
•
reset
7
votes
6
replies
5.6k
views
How to use brainarray custom cdf with oligo package?
oligo
customcdf
HTA
frma
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
sanj
▴ 20
0
votes
2
replies
4.7k
views
Normalization before ComBat
Microarray
Normalization
probe
affy
frma
Microarray
Normalization
probe
affy
frma
updated 10.6 years ago by
francesco.brundu@gmail.com
▴ 40 • written 10.6 years ago by
W. Evan Johnson
▴ 850
0
votes
6
replies
3.2k
views
converting probeset id to gene id's : fRMA
probe
affy
convert
frma
probe
affy
convert
frma
updated 9.9 years ago by
Peter Langfelder
★ 3.0k • written 9.9 years ago by
Abhishek Pratap
▴ 190
0
votes
6
replies
3.0k
views
processing Illumina HT12v4.0 expression data from GEO
Normalization
affy
PROcess
GEOquery
frma
Normalization
affy
PROcess
GEOquery
frma
updated 9.8 years ago by
Sean Davis
21k • written 9.8 years ago by
Abhishek Pratap
▴ 190
0
votes
9
replies
2.7k
views
frma and alternative CDFs
GO
cdf
frma
BRAIN
GO
cdf
frma
BRAIN
updated 9.8 years ago by
Matthew McCall
▴ 830 • written 9.8 years ago by
Guest User
★ 13k
0
votes
0
replies
2.6k
views
Seperate quantile normalization but common probe summary by median polish (oligo package)?
Normalization
probe
oligo
frma
frmaTools
Normalization
probe
oligo
frma
frmaTools
11.8 years ago
Schott, Johanna
▴ 20
2
votes
8
replies
2.5k
views
frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?
frma
frmatools
updated 9.3 years ago by
Matthew McCall
▴ 830 • written 9.3 years ago by
Ryan C. Thompson
★ 7.9k
2
votes
3
replies
2.4k
views
hgu133plus2hsentrezgcdf or hgu133ahsentrezgcdf packages not installing
readaffy
frma
affy
package installation
hgu133a
6.1 years ago
Chris Mancuso
• 0
0
votes
9
replies
2.4k
views
using frma and brainarray cdf on exon arrays
cdf
affy
PROcess
oligo
xps
frma
cdf
affy
PROcess
oligo
xps
frma
updated 10.3 years ago by
Stephen Piccolo
▴ 590 • written 10.3 years ago by
Ty Thomson
▴ 100
3
votes
9
replies
1.9k
views
About the best use of frma for several GEO Series
frma
normalization
preprocessing
updated 7.4 years ago by
Matthew McCall
▴ 830 • written 7.4 years ago by
ctruntzer
▴ 20
1
vote
5
replies
1.9k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma
bioconductor
batcheffect
Primeview
insilicomerging
updated 9.1 years ago by
Matthew McCall
▴ 830 • written 9.1 years ago by
svlachavas
▴ 830
0
votes
1
reply
1.9k
views
fRMA for Gene ST arrays
Microarray
probe
oligo
frma
Microarray
probe
oligo
frma
updated 10.3 years ago by
Matthew McCall
▴ 830 • written 10.3 years ago by
maria
▴ 10
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
5
replies
1.8k
views
fRMA: Applying mouse4302frmavecs on HT_MG-430_PM Arrays
frma
microarray
affiymetrix
8.3 years ago
Matthias Z.
▴ 20
0
votes
5
replies
1.7k
views
SCAN.UPC for Illumina arrays?
RNASeq
qPCR
affy
oligo
frma
RNASeq
qPCR
affy
oligo
frma
updated 10.5 years ago by
Stephen Piccolo
▴ 590 • written 10.5 years ago by
Tim Triche
★ 4.2k
0
votes
3
replies
1.7k
views
Using fRMA with "alternative" CDF files
Normalization
cdf
frma
Normalization
cdf
frma
updated 11.3 years ago by
Matthew McCall
▴ 830 • written 11.3 years ago by
Cornwell, Adam
▴ 110
3
votes
1
reply
1.7k
views
Processing several GSM from GEO database using Barcode and fRMA
frma
barcode
geneexpression
gsm
ncbi geo
updated 6.5 years ago by
Matthew McCall
▴ 830 • written 6.5 years ago by
diana.elassal
• 0
0
votes
4
replies
1.6k
views
fRMA error - unable to create unique mapping
frma
frmatools
affy
updated 7.6 years ago by
Matthew McCall
▴ 830 • written 7.6 years ago by
yesitsjess
• 0
0
votes
2
replies
1.6k
views
frma normalization and batch effects
Normalization
frma
Normalization
frma
updated 10.7 years ago by
Wolfgang Huber
★ 13k • written 10.7 years ago by
Guest User
★ 13k
0
votes
3
replies
1.6k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools
FRMA
affyio
AffymetrixDataTestFiles
affy
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Seymoo
• 0
0
votes
6
replies
1.6k
views
barcode with custom CDF
cdf
frma
frmaTools
cdf
frma
frmaTools
updated 11.1 years ago by
Stephen Piccolo
▴ 590 • written 11.1 years ago by
Guest User
★ 13k
0
votes
2
replies
1.5k
views
barcode support for other platforms
frma
updated 9.7 years ago by
Matthew McCall
▴ 830 • written 9.7 years ago by
Guest User
★ 13k
0
votes
3
replies
1.5k
views
frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
frma
affymetrix
barcode
updated 8.3 years ago by
Matthew McCall
▴ 830 • written 8.3 years ago by
minnie
• 0
0
votes
2
replies
1.5k
views
frma for Nimblegen arrays?
Microarray
Annotation
Normalization
affy
PROcess
safe
frma
frmaTools
Microarray
affy
updated 11.5 years ago by
Benilton Carvalho
★ 4.3k • written 11.5 years ago by
wrighth
▴ 260
0
votes
5
replies
1.5k
views
How to normalize mouse gene 1.0st arry using frma?
microarray
frma
updated 6.2 years ago by
emacreamoinn
• 0 • written 7.0 years ago by
aritra
• 0
0
votes
1
reply
1.5k
views
fRMA- more issues with custom CDFs
GO
probe
frma
GO
probe
frma
updated 10.1 years ago by
Matthew McCall
▴ 830 • written 10.1 years ago by
Cornwell, Adam
▴ 110
0
votes
4
replies
1.4k
views
errors in FRMA
Annotation
hgu133a2
hgu133a
frma
Annotation
hgu133a2
hgu133a
frma
updated 12.0 years ago by
Matthew McCall
▴ 830 • written 12.0 years ago by
Mayte Suarez-Farinas
▴ 510
0
votes
5
replies
1.4k
views
frma for Nimblegen arrays?
Microarray
Normalization
affy
PROcess
safe
frma
Microarray
Normalization
affy
PROcess
updated 11.5 years ago by
Matthew McCall
▴ 830 • written 11.5 years ago by
wrighth
▴ 260
1
vote
3
replies
1.4k
views
Problem with frma median_polish
software error
frma
updated 8.6 years ago by
Matthew McCall
▴ 830 • written 8.6 years ago by
Thomas Pfau
▴ 20
2
votes
2
replies
1.4k
views
Strategies for fRMA on custom dataset(s)?
frma
frmatools
updated 9.3 years ago by
Matthew McCall
▴ 830 • written 9.3 years ago by
Ryan C. Thompson
★ 7.9k
4
votes
5
replies
1.4k
views
fRMA results different for Windows and Linux
frma
expr
gene expression data
affy
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
osieman52
• 0
0
votes
3
replies
1.4k
views
GCRMA: feature request
GO
Regression
probe
gcrma
frma
GO
Regression
probe
gcrma
frma
updated 13.3 years ago by
Björn Usadel
▴ 250 • written 13.3 years ago by
Guido Hooiveld
★ 3.9k
0
votes
0
replies
1.4k
views
FW: fRMA package
affxparser
frma
GenomicRanges
affxparser
frma
GenomicRanges
10.8 years ago
Li Liu
▴ 100
0
votes
3
replies
1.3k
views
fRMA normalization for Mouse Gene 2.1 ST Array
frma
affymetrix mouse gene arrays
updated 7.0 years ago by
Matthew McCall
▴ 830 • written 7.0 years ago by
arisarkar88
▴ 40
0
votes
1
reply
1.2k
views
FrozenRMA how to
Microarray
Network
hgu133plus2
Biobase
PROcess
KEGGSOAP
beadarray
EBImage
edgeR
frma
updated 12.2 years ago by
Matthew McCall
▴ 830 • written 12.2 years ago by
Alex Sanchez
▴ 20
0
votes
2
replies
1.2k
views
How many arrays are "enough" for creating useful fRMA vectors?
annotation
frma
frmatools
updated 9.4 years ago by
Matthew McCall
▴ 830 • written 9.4 years ago by
Tim Triche
★ 4.2k
0
votes
0
replies
1.2k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO
probe
PROcess
frma
GO
probe
PROcess
frma
9.9 years ago
Matthew McCall
▴ 830
0
votes
2
replies
1.2k
views
New Bioconductor Package: SCAN.UPC
Normalization
affy
frma
Normalization
affy
frma
updated 11.6 years ago by
Stephen Piccolo
▴ 590 • written 11.6 years ago by
W. Evan Johnson
▴ 850
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
1.2k
views
fRMA- more issues with custom CDFs
GO
probe
frma
GO
probe
frma
updated 10.2 years ago by
Matthew McCall
▴ 830 • written 10.2 years ago by
Cornwell, Adam
▴ 110
0
votes
0
replies
1.2k
views
Annotation discrepancy HT HGU 133+ PM chip
probe
frma
probe
frma
10.4 years ago
Eric Zollars
▴ 30
0
votes
2
replies
1.2k
views
looking for data file for ATH1 (GPL198)
PROcess
frma
PROcess
frma
updated 10.6 years ago by
Loraine, Ann
▴ 50 • written 10.6 years ago by
Matthew McCall
▴ 830
0
votes
1
reply
1.2k
views
fRMA without using ReadAffy()
frma
SCAN.UPC
frma
SCAN.UPC
updated 11.0 years ago by
Matthew McCall
▴ 830 • written 11.0 years ago by
S.D. Chorlton
▴ 10
0
votes
0
replies
1.1k
views
In the frmaTools package, how can I makeVectorsFeatureSet() output include probeVecCore like the pre-built vectors?
frma
frmatools
affymetrix microarrays
8.1 years ago
jperezrogers
• 0
1
vote
4
replies
1.1k
views
Summarization probe ID to gene : FRMA
summarization
FRMA
affy
updated 7.5 years ago by
James W. MacDonald
65k • written 7.5 years ago by
Shamim Sarhadi
▴ 20
0
votes
1
reply
1.1k
views
fRMA for Gene ST arrays
affy
oligo
frma
ASSIGN
affy
oligo
frma
ASSIGN
updated 11.1 years ago by
Matthew McCall
▴ 830 • written 11.1 years ago by
Kamila Naxerova
▴ 100
0
votes
1
reply
1.1k
views
Seperate quantile normalization but common probe summary by median polish (oligo package)?
Normalization
probe
frma
frmaTools
Normalization
probe
frma
frmaTools
updated 11.8 years ago by
James W. MacDonald
65k • written 11.8 years ago by
Guest User
★ 13k
0
votes
2
replies
1.1k
views
fRMA error when using exprs()
Normalization
frma
Normalization
frma
12.7 years ago
SylvainBrohée
▴ 50
0
votes
1
reply
1.1k
views
frmaTools library error :: makeVectorsAffyBatch() function
Microarray
probe
frma
frmaTools
Microarray
probe
frma
frmaTools
updated 10.9 years ago by
Matthew McCall
▴ 830 • written 10.9 years ago by
Tae-Hoon Chung
▴ 70
0
votes
0
replies
1.1k
views
回复: Re: fRMA package
affxparser
frma
GenomicRanges
affxparser
frma
GenomicRanges
10.8 years ago
Hanyine
▴ 30
50 results • Page
1 of 1
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Replies
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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