Package 'SpikeInSubset'

Cross hybridizers

Description

Probe Sets likely to crosshybridize to spiked-in probesets in the Affymetrix HGU133A spike in

This objact is list. Each component of the list contains probeset names of possible crosshybridizers. The sequences of each spiked-in clone were collected and blasted against all HG-U133A target sequences. Target sequences are the ~600bp regions from which probes were selected. Thresholds of 100, 150 and 200bp were used and define the three components of the list.

Usage

data(hgu133a.spikein.xhyb)

Format

A list

Source

Simon Cawley [email protected]

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Subset of Affymetrix SpikeIn Experiment Data

Description

Probe-level and pre-proecssed data for six arrays (two triplicates) from the HGU95 and HGU133 SpikeIn experiments.

Usage

data(spikein95)
data(rma95)
data(mas95)

data(spikein133)
data(rma133)
data(mas133)

Format

SpikeIn is ProbeSet containing the $PM$ and $MM$ intensities for a gene spiked in at different concentrations. Use pData to see the cosntrations.

Source

spikein95 and spikein133 are instances of ProbeSet with the probe-level data for six arrays (two triplicates) from the HGU95 and HGU133 SpikeIn experiments respectively. rma95 and rma133 contain the data pre-processed with RMA. mas95 and mas133 contain the data preprocssed with mas5 (expression and present/absent calls). The calls are in objects called pacalls95 and pacalls133.

For more information see Irizarry, R.A., et al. NAR (2003) http://www.biostat.jhsph.edu/~ririzarr/papers/index.html

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