[BioC] filtered Exon Arrays: Core vs Extended Dataset
Lana Schaffer
schaffer at scripps.edu
Wed May 6 22:55:25 CEST 2009
Hi,
I have used Limma with both the core (~17,000) and extended (~120,000)
Affymetrix datasets. Do you think that significant transcripts in the
core dataset would also be found to be significant in the extended
dataset?
I have found that ~88% of the significant expressed transcripts from the
core dataset are not found in the significant expressed transcripts from
the extended dataset.
Furthermore, 86% (1352/1575) of those significant core transcripts are
found in the
filtered extended dataset (input to Limma), but are not found to be
significant in the filtered extended dataset.
Core Extended
Intersection
Limma:adj.pvalue=0.05 1575 1142
225
overlap extended filtered dataset 1352 (86%)
datasets 17,939 112,213
filtered datasets 17,939 61,717
Filtering was performed by standard deviation according to the
following code.
rs = rowSds(GL.un)
lambda = 0.45
filtered = GL.un[ rs > quantile(rs, lambda, na.rm=T), ]
What are your suggestions for this discrepancy?
Lana Schaffer
Biostatistics/Informatics
The Scripps Research Institute
DNA Array Core Facility
La Jolla, CA 92037
(858) 784-2263
(858) 784-2994
schaffer at scripps.edu
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