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Limma p-values, fdr and classifyTests
limma
updated 5.2 years ago by 50k • written 19.7 years ago by ▴ 940
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1.1k
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ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe affy probe affy
updated 5.3 years ago by 0 • written 20.2 years ago by ▴ 940
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1.2k
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double violation of normalization assumptions?
Microarray Normalization probe limma gcrma Microarray Normalization probe limma gcrma
18.2 years ago Matthew Hannah ▴ 940
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1.9k
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Answer: A: Biological replication (was RNA degradation problem)
18.3 years ago Matthew Hannah ▴ 940
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1.9k
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Answer: A: Biological replication (was RNA degradation problem)
18.3 years ago Matthew Hannah ▴ 940
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0
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1.9k
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Answer: A: Biological replication (was RNA degradation problem)
18.3 years ago Matthew Hannah ▴ 940
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0
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1.3k
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Answer: A: RNA degradation problem
18.3 years ago Matthew Hannah ▴ 940
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1
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1.1k
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RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 18.3 years ago by ▴ 810 • written 18.3 years ago by ▴ 940
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853
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PLIER affinities redux
ath1121501 cdf probe Biobase affy plier ath1121501 cdf probe Biobase affy plier
18.5 years ago Matthew Hannah ▴ 940
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1.1k
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permutation/resampling FDR correction
Regression limma Regression limma
18.8 years ago Matthew Hannah ▴ 940
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1
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758
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Wilcoxon test [was loged data or not loged previous to use normalize.quantile]
updated 19.0 years ago by ▴ 210 • written 19.0 years ago by ▴ 940
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1
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1.7k
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Answer: A: no BioConductor posting guide
19.0 years ago Matthew Hannah ▴ 940
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0
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1.6k
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Answer: A: Cy3 Cy5 mixup?
19.0 years ago Matthew Hannah ▴ 940
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0
replies
991
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limma regression / fdr permutation correction
19.1 years ago Matthew Hannah ▴ 940
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0
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1.3k
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Answer: A: p-value adjustment
19.1 years ago Matthew Hannah ▴ 940
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0
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2.0k
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Answer: A: Order in which ReadAffy() and read.affybatch()
19.1 years ago Matthew Hannah ▴ 940
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1
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944
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GCRMA: low intensity exprs estimates / pval distributions
gcrma gcrma
19.1 years ago Matthew Hannah ▴ 940
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0
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944
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Answer: A: GCRMA: low intensity exprs estimates / pval distributions
19.1 years ago Matthew Hannah ▴ 940
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0
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883
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RMA verse GCRMA, low intensity
cycle cycle
19.1 years ago Matthew Hannah ▴ 940
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1
reply
1.3k
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kyte and doolittle hydropathy values/plot - sub + sliding window mean
graph convert graph convert
19.4 years ago Matthew Hannah ▴ 940
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0
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1.3k
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Answer: A: kyte and doolittle hydropathy values/plot - sub + sliding window mean
19.4 years ago Matthew Hannah ▴ 940
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0
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875
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limma p.values, tech replication and dup cor
affy limma oligo affy limma oligo
19.5 years ago Matthew Hannah ▴ 940
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0
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643
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gcrma - all low value output - error somewhere?
cdf affy gcrma matchprobes cdf affy gcrma matchprobes
19.5 years ago Matthew Hannah ▴ 940
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1
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816
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gcrma.bg.transformation missing
gcrma gcrma
updated 19.5 years ago by ▴ 410 • written 19.5 years ago by ▴ 940
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1
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405
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agcdf / atgenome1probe
updated 19.5 years ago by ▴ 950 • written 19.5 years ago by ▴ 940
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0
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879
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Answer: A: P value for each probe
19.5 years ago Matthew Hannah ▴ 940
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0
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650
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Limma with multiple samples but only 2 reps
limma limma
19.6 years ago Matthew Hannah ▴ 940
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0
replies
603
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ULYSIS Alexa Fluor labelling kit / dye bias / limma
limma limma
19.6 years ago Matthew Hannah ▴ 940
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0
replies
724
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Limma p-value distributions, false +ve/-ve etc...
limma limma
19.6 years ago Matthew Hannah ▴ 940
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3
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3.7k
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Selecting p-value cutoffs for differential expression
limma gcrma limma gcrma
updated 19.6 years ago by ▴ 20 • written 19.6 years ago by ▴ 940
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1.4k
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RE: Normalising divergent samples.
Microarray Normalization affy limma gcrma Microarray Normalization affy limma gcrma
19.6 years ago Matthew Hannah ▴ 940
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1
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1.3k
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Normalising divergent samples.
Microarray Normalization affy limma gcrma Microarray Normalization affy limma gcrma
updated 19.6 years ago by ▴ 620 • written 19.6 years ago by ▴ 940
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1
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1.1k
views
Answer: A: Error with library(limma) with R2.0 devel
19.6 years ago Matthew Hannah ▴ 940
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4
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1.1k
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Error with library(limma) with R2.0 devel
limma limma
19.6 years ago Matthew Hannah ▴ 940
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0
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1.6k
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Answer: A: RE: RMA normalization
19.6 years ago Matthew Hannah ▴ 940
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0
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1.4k
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Answer: A: MAS5 and GCOC difference to get CEL files
19.6 years ago Matthew Hannah ▴ 940
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1
reply
1.0k
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Errors w/ getBioC(develOK =TRUE) with R2.0 devel
aCGH GO Biobase DynDoc annotate edd genefilter geneplotter rhdf5 multtest ctc ROC affy
19.6 years ago Matthew Hannah ▴ 940
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0
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1.0k
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Answer: A: Errors w/ getBioC(develOK =TRUE) with R2.0 devel
19.6 years ago Matthew Hannah ▴ 940
0
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0
replies
602
views
Affymetrix is changing its labelling kit - data analysis will change!?
affy affy
19.6 years ago Matthew Hannah ▴ 940
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0
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869
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Do I now understand Limma contrast matrices??
19.6 years ago Matthew Hannah ▴ 940
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0
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869
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GCRMA/RMA bimodal distribution
drosgenome1 limma gcrma drosgenome1 limma gcrma
19.6 years ago Matthew Hannah ▴ 940
0
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5
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1.2k
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GCRMA/RMA bimodal distribution
gcrma gcrma
updated 19.6 years ago by ★ 6.0k • written 19.7 years ago by ▴ 940
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0
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1.2k
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Answer: A: GCRMA/RMA bimodal distribution
19.6 years ago Matthew Hannah ▴ 940
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0
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1.0k
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Errors w/ getBioC()
aCGH GO Biobase DynDoc annotate edd genefilter geneplotter rhdf5 multtest ctc ROC affy
19.6 years ago Matthew Hannah ▴ 940
0
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0
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1.0k
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Unexpected results using limma with numerical factor - regression intercept?
GO Regression limma GO Regression limma
19.7 years ago Matthew Hannah ▴ 940
0
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1
reply
928
views
FW: Limma p-values, fdr and classifyTests
limma limma
updated 19.7 years ago by 50k • written 19.7 years ago by ▴ 940
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0
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840
views
Answer: A: Unexpected results using limma with numerical factor
19.7 years ago Matthew Hannah ▴ 940
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0
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925
views
RE: Design matrix with multiple genotypes + quantified variables (+cor/regression)
Regression limma Regression limma
19.7 years ago Matthew Hannah ▴ 940
0
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0
replies
563
views
AffyPLM can detect poor labelling on test chips
affy affy
19.7 years ago Matthew Hannah ▴ 940
0
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0
replies
669
views
Design matrix with multiple genotypes + quantified variables
Regression Regression
19.7 years ago Matthew Hannah ▴ 940
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