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Limma p-values, fdr and classifyTests
limma
updated 4.8 years ago by 49k • written 19.3 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 4.9 years ago by 0 • written 19.8 years ago by ▴ 940
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0
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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
17.9 years ago Matthew Hannah ▴ 940
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0
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1.7k
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Answer: A: Biological replication (was RNA degradation problem)
17.9 years ago Matthew Hannah ▴ 940
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0
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1.7k
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Answer: A: Biological replication (was RNA degradation problem)
17.9 years ago Matthew Hannah ▴ 940
0
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0
replies
1.7k
views
Answer: A: Biological replication (was RNA degradation problem)
17.9 years ago Matthew Hannah ▴ 940
0
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0
replies
1.2k
views
Answer: A: RNA degradation problem
17.9 years ago Matthew Hannah ▴ 940
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1
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985
views
RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 17.9 years ago by ▴ 810 • written 17.9 years ago by ▴ 940
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0
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788
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PLIER affinities redux
ath1121501 cdf probe Biobase affy plier ath1121501 cdf probe Biobase affy plier
18.2 years ago Matthew Hannah ▴ 940
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0
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1.0k
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permutation/resampling FDR correction
Regression limma Regression limma
18.4 years ago Matthew Hannah ▴ 940
0
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1
reply
690
views
Wilcoxon test [was loged data or not loged previous to use normalize.quantile]
updated 18.7 years ago by ▴ 210 • written 18.7 years ago by ▴ 940
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1
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1.5k
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Answer: A: no BioConductor posting guide
18.7 years ago Matthew Hannah ▴ 940
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0
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1.5k
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Answer: A: Cy3 Cy5 mixup?
18.7 years ago Matthew Hannah ▴ 940
0
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0
replies
936
views
limma regression / fdr permutation correction
18.7 years ago Matthew Hannah ▴ 940
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0
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1.2k
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Answer: A: p-value adjustment
18.7 years ago Matthew Hannah ▴ 940
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0
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1.8k
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Answer: A: Order in which ReadAffy() and read.affybatch()
18.7 years ago Matthew Hannah ▴ 940
0
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1
reply
886
views
GCRMA: low intensity exprs estimates / pval distributions
gcrma gcrma
18.8 years ago Matthew Hannah ▴ 940
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0
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886
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Answer: A: GCRMA: low intensity exprs estimates / pval distributions
18.8 years ago Matthew Hannah ▴ 940
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0
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822
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RMA verse GCRMA, low intensity
cycle cycle
18.8 years ago Matthew Hannah ▴ 940
0
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1
reply
1.2k
views
kyte and doolittle hydropathy values/plot - sub + sliding window mean
graph convert graph convert
19.0 years ago Matthew Hannah ▴ 940
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0
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1.2k
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Answer: A: kyte and doolittle hydropathy values/plot - sub + sliding window mean
19.0 years ago Matthew Hannah ▴ 940
0
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0
replies
821
views
limma p.values, tech replication and dup cor
affy limma oligo affy limma oligo
19.1 years ago Matthew Hannah ▴ 940
0
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0
replies
622
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gcrma - all low value output - error somewhere?
cdf affy gcrma matchprobes cdf affy gcrma matchprobes
19.1 years ago Matthew Hannah ▴ 940
0
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1
reply
748
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gcrma.bg.transformation missing
gcrma gcrma
updated 19.1 years ago by ▴ 410 • written 19.1 years ago by ▴ 940
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1
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362
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agcdf / atgenome1probe
updated 19.2 years ago by ▴ 950 • written 19.2 years ago by ▴ 940
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0
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794
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Answer: A: P value for each probe
19.2 years ago Matthew Hannah ▴ 940
0
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0
replies
579
views
Limma with multiple samples but only 2 reps
limma limma
19.2 years ago Matthew Hannah ▴ 940
0
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0
replies
539
views
ULYSIS Alexa Fluor labelling kit / dye bias / limma
limma limma
19.2 years ago Matthew Hannah ▴ 940
0
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0
replies
676
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Limma p-value distributions, false +ve/-ve etc...
limma limma
19.2 years ago Matthew Hannah ▴ 940
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3
replies
3.5k
views
Selecting p-value cutoffs for differential expression
limma gcrma limma gcrma
updated 19.2 years ago by ▴ 20 • written 19.3 years ago by ▴ 940
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0
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1.4k
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RE: Normalising divergent samples.
Microarray Normalization affy limma gcrma Microarray Normalization affy limma gcrma
19.2 years ago Matthew Hannah ▴ 940
0
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1
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1.2k
views
Normalising divergent samples.
Microarray Normalization affy limma gcrma Microarray Normalization affy limma gcrma
updated 19.2 years ago by ▴ 620 • written 19.2 years ago by ▴ 940
0
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1
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1.0k
views
Answer: A: Error with library(limma) with R2.0 devel
19.2 years ago Matthew Hannah ▴ 940
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4
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1.0k
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Error with library(limma) with R2.0 devel
limma limma
19.3 years ago • updated 19.2 years ago Matthew Hannah ▴ 940
0
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0
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1.5k
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Answer: A: RE: RMA normalization
19.2 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
19.2 years ago Matthew Hannah ▴ 940
0
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1
reply
953
views
Errors w/ getBioC(develOK =TRUE) with R2.0 devel
aCGH GO Biobase DynDoc annotate edd genefilter geneplotter rhdf5 multtest ctc ROC affy
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
953
views
Answer: A: Errors w/ getBioC(develOK =TRUE) with R2.0 devel
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
555
views
Affymetrix is changing its labelling kit - data analysis will change!?
affy affy
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
803
views
Do I now understand Limma contrast matrices??
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
805
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GCRMA/RMA bimodal distribution
drosgenome1 limma gcrma drosgenome1 limma gcrma
19.3 years ago Matthew Hannah ▴ 940
0
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5
replies
1.1k
views
GCRMA/RMA bimodal distribution
gcrma gcrma
updated 19.3 years ago by ★ 6.0k • written 19.3 years ago by ▴ 940
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0
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1.1k
views
Answer: A: GCRMA/RMA bimodal distribution
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
930
views
Errors w/ getBioC()
aCGH GO Biobase DynDoc annotate edd genefilter geneplotter rhdf5 multtest ctc ROC affy
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
958
views
Unexpected results using limma with numerical factor - regression intercept?
GO Regression limma GO Regression limma
19.3 years ago Matthew Hannah ▴ 940
0
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1
reply
857
views
FW: Limma p-values, fdr and classifyTests
limma limma
updated 19.3 years ago by 49k • written 19.3 years ago by ▴ 940
0
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0
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761
views
Answer: A: Unexpected results using limma with numerical factor
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
867
views
RE: Design matrix with multiple genotypes + quantified variables (+cor/regression)
Regression limma Regression limma
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
520
views
AffyPLM can detect poor labelling on test chips
affy affy
19.3 years ago Matthew Hannah ▴ 940
0
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0
replies
615
views
Design matrix with multiple genotypes + quantified variables
Regression Regression
19.3 years ago Matthew Hannah ▴ 940
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