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Views
Votes
Showing :
plier
•
reset
0
votes
0
replies
856
views
Affymetrix gene st array - ok to do statistics on Category:Main only?
limma
plier
oligo
limma
plier
oligo
11.1 years ago
Martin O'Hare
▴ 10
0
votes
0
replies
912
views
FARMS package (fwd)
Microarray
Normalization
cdf
plier
farms
Microarray
Normalization
cdf
plier
farms
11.2 years ago
Günter Klambauer
▴ 540
0
votes
0
replies
666
views
plier package
Normalization
cdf
plier
Normalization
cdf
plier
11.2 years ago
fire1976 wyoming
▴ 380
0
votes
0
replies
704
views
XPS package working with Affymetrix GeneChip 1.0 ST at gene level
cdf
affy
plier
xps
cdf
affy
plier
xps
11.3 years ago
cstrato
★ 3.9k
0
votes
1
reply
962
views
No changes between Groups using GeneST Arrays from Affymetrix
GO
vsn
plier
GO
vsn
plier
updated 13.4 years ago by
Mike Walter
▴ 230 • written 13.5 years ago by
Benjamin Otto
▴ 830
0
votes
1
reply
1.1k
views
Prokaryotic_Rhodobacter capsulatus GEP
Epigenetics
cdf
affy
makecdfenv
plier
affxparser
preprocessCore
Epigenetics
cdf
affy
updated 14.8 years ago by
dorothyc
▴ 140 • written 14.8 years ago by
James W. MacDonald
63k
0
votes
2
replies
901
views
Prokaryotic_Rhodobacter capsulatus GEP
cdf
plier
cdf
plier
updated 14.8 years ago by
Martin Morgan
25k • written 14.8 years ago by
dorothyc
▴ 140
0
votes
1
reply
1.0k
views
Normalization Recommendations- severe biological variation (from the digest)
Normalization
vsn
plier
Normalization
vsn
plier
updated 15.3 years ago by
Naomi Altman
★ 6.0k • written 15.3 years ago by
Nick Henriquez
▴ 20
0
votes
3
replies
841
views
Standard error in summarization ExpressionSets
plier
plier
updated 15.3 years ago by
James W. MacDonald
63k • written 15.3 years ago by
Rodrigo Santamaría Vicente
▴ 10
0
votes
0
replies
733
views
plier using reference set normalization
Normalization
plier
RefPlus
Normalization
plier
RefPlus
15.6 years ago
Roumyana Yordanova
▴ 110
0
votes
3
replies
1.1k
views
RMA, d-chip and Plier for new chip type Human/Mouse/Rat Gene
plier
plier
updated 15.6 years ago by
Henrik Bengtsson
★ 2.4k • written 15.6 years ago by
Fang, Hong*
▴ 30
0
votes
0
replies
842
views
problem with function to interrogate x:Map (exonmap)
Survival
genefilter
affy
plier
affyio
exonmap
Survival
genefilter
affy
plier
affyio
16.0 years ago
Wolfgang Raffelsberger
▴ 160
0
votes
4
replies
1.1k
views
problems rma() with mouse exon affy data in exonmap package
Survival
cdf
genefilter
affy
simpleaffy
plier
exonmap
Survival
cdf
genefilter
affy
updated 16.1 years ago by
James W. MacDonald
63k • written 16.1 years ago by
bruce
▴ 20
0
votes
1
reply
980
views
Exonmap mapping problems
Survival
genefilter
affy
plier
affyio
exonmap
Survival
genefilter
affy
plier
affyio
updated 16.1 years ago by
Michal Okoniewski
▴ 120 • written 16.1 years ago by
Tore Eriksson
▴ 10
0
votes
0
replies
670
views
justPlier() on UNIX
plier
plier
16.3 years ago
Pickard, Mike
▴ 10
0
votes
6
replies
1.2k
views
Affy EXON Array: iterPLIER or RMA
Cancer
plier
Cancer
plier
updated 16.4 years ago by
James W. MacDonald
63k • written 16.4 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
1.0k
views
annaffy errors
GO
Survival
mgu74av2
cdf
annotate
affy
limma
gcrma
matchprobes
annaffy
simpleaffy
plier
updated 16.7 years ago by
James W. MacDonald
63k • written 16.7 years ago by
Ido M. Tamir
▴ 320
0
votes
0
replies
716
views
questions on BioC's implementation of plier
Normalization
plier
Normalization
plier
16.7 years ago
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.3k
views
results of justPlier vs. RMA
Clustering
affy
plier
affyio
Clustering
affy
plier
affyio
updated 16.9 years ago by
Michal Okoniewski
▴ 120 • written 16.9 years ago by
He, Yiwen NIH/CIT
▴ 360
0
votes
1
reply
747
views
Mismatch probe handling for exon arrays
Cancer
Breast
probe
affy
plier
Cancer
Breast
probe
affy
plier
updated 17.0 years ago by
James W. MacDonald
63k • written 17.0 years ago by
Steven McKinney
▴ 310
0
votes
2
replies
918
views
plier error
plier
plier
updated 17.1 years ago by
Crispin Miller
★ 1.1k • written 17.1 years ago by
D.Enrique ESCOBAR ESPINOZA
▴ 360
0
votes
0
replies
616
views
help with justPlier
plier
plier
17.1 years ago
He, Yiwen NIH/CIT
▴ 360
0
votes
8
replies
1.3k
views
error message in gcrma
cdf
affy
gcrma
matchprobes
plier
cdf
affy
gcrma
matchprobes
plier
updated 17.3 years ago by
Seth Falcon
★ 7.4k • written 17.3 years ago by
Mohammad Esad-Djou
▴ 520
0
votes
2
replies
657
views
Affymetrix question
plier
plier
updated 17.9 years ago by
James W. MacDonald
63k • written 17.9 years ago by
lucia ¿?
▴ 50
0
votes
5
replies
1.3k
views
PLIER affinities redux
cdf
probe
Biobase
affy
plier
cdf
probe
Biobase
affy
plier
updated 17.9 years ago by
Crispin Miller
★ 1.1k • written 18.0 years ago by
Jeremy Gollub
▴ 60
0
votes
0
replies
747
views
PLIER affinities redux
ath1121501
cdf
probe
Biobase
affy
plier
ath1121501
cdf
probe
Biobase
affy
plier
18.0 years ago
Matthew Hannah
▴ 940
0
votes
1
reply
793
views
PLIER affinities
rae230a
cdf
probe
reposTools
affy
plier
rae230a
cdf
probe
reposTools
affy
plier
updated 18.0 years ago by
James W. MacDonald
63k • written 18.0 years ago by
Jeremy Gollub
▴ 80
0
votes
1
reply
657
views
Problems with justGCRMA: Error in bg.adjust.fullmodel
vsn
gcrma
matchprobes
plier
vsn
gcrma
matchprobes
plier
updated 18.1 years ago by
James W. MacDonald
63k • written 18.1 years ago by
Jordi Altirriba Gutiérrez
▴ 350
0
votes
0
replies
1.2k
views
NA values
Normalization
Cancer
limma
gcrma
affyPLM
limmaGUI
plier
Normalization
Cancer
limma
gcrma
18.2 years ago
Brooke-Powell, Elizabeth
▴ 170
0
votes
2
replies
814
views
PLIER: two questions
plier
plier
updated 18.2 years ago by
Adaikalavan Ramasamy
★ 1.8k • written 18.2 years ago by
Ariel Chernomoretz
▴ 380
0
votes
3
replies
914
views
Anyone get plier to install on OS X?
plier
plier
18.3 years ago
Ken Termiso
▴ 250
0
votes
1
reply
652
views
PLIER -- low values?
Microarray
plier
Microarray
plier
updated 18.3 years ago by
James W. MacDonald
63k • written 18.3 years ago by
Tarun Nayar
▴ 190
0
votes
1
reply
736
views
plier crashes with 51 CEL files
gcrma
PROcess
plier
gcrma
PROcess
plier
18.5 years ago
Adaikalavan Ramasamy
★ 1.8k
0
votes
0
replies
537
views
Re:PLIER wierd Mvs A
plier
plier
18.6 years ago
Anthony Bosco
▴ 20
0
votes
1
reply
905
views
PLIER Error
plier
plier
updated 18.6 years ago by
Crispin Miller
★ 1.1k • written 18.6 years ago by
Anthony Bosco
▴ 500
0
votes
0
replies
720
views
PLIER
plier
plier
18.6 years ago
Crispin Miller
★ 1.1k
0
votes
0
replies
688
views
MAS5+32, PLIER+16 alorithms reported in affycomp
Normalization
probe
affycomp
plier
Normalization
probe
affycomp
plier
18.6 years ago
Ariel Chernomoretz
▴ 380
0
votes
2
replies
790
views
Affy PLIER
plier
plier
updated 19.0 years ago by
Rafael A. Irizarry
2.3k • written 19.0 years ago by
Dick Beyer
★ 1.4k
0
votes
1
reply
928
views
PLIER is available as open source
plier
SANTA
plier
SANTA
updated 19.0 years ago by
Francois Collin
▴ 50 • written 19.0 years ago by
Lelivelt, Mike
▴ 50
0
votes
3
replies
2.5k
views
what normalization method does mas5 use
Normalization
GO
affy
gcrma
plier
Normalization
GO
affy
gcrma
plier
updated 19.2 years ago by
F Duan
▴ 100 • written 19.2 years ago by
Brian Bennett
▴ 10
0
votes
0
replies
819
views
Question regarding bg correction/normalization/summarization
Normalization
Cancer
probe
affy
vsn
plier
Normalization
Cancer
probe
affy
vsn
plier
19.2 years ago
Wolfgang Huber
13k
0
votes
2
replies
852
views
Running justRMA on .CEL files in another directory
plier
plier
updated 19.3 years ago by
donghu@itsa.ucsf.edu
▴ 70 • written 19.3 years ago by
PARK,CHRISTOPHER CHANGSUN
▴ 50
0
votes
0
replies
1.1k
views
median polish vs mas/PLIER info
Microarray
Normalization
Cancer
probe
affy
GeneSpring
PROcess
plier
Microarray
Cancer
19.4 years ago
Anthony Bosco
▴ 500
0
votes
1
reply
769
views
AFFY PLIER ALGORITHM
plier
plier
19.5 years ago
Anthony Bosco
▴ 500
44 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
James W. MacDonald
63k
No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
• 0
Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …
Votes
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Remove duplicates of colData in TreeSummarizedExperiment
Answer: Remove duplicates of colData in TreeSummarizedExperiment
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