metaplasia: Intestinal Metaplasia Dataset

In adele/omicsMA: Variance-Preserving Estimation and Normalization of M-A Values

Description

This is part of the dataset used in the study by \insertCiteribeiro2019omicsMAomicsMA.

Usage

metaplasia

Format

A list with the following elements:

R.mean

A 45015 x 10 matrix with the means of the red (test) foreground pixels in each spot of each array.

G.mean

A 45015 x 10 matrix with the means of the green (reference) foreground pixels in each spot of each array.

R.var

A 45015 x 10 matrix with the variances across red foreground pixels in each spot of each array.

G.var

A 45015 x 10 matrix with the variances across green foreground pixels in each spot of each array.

RG.cov

A 45015 x 10 matrix with the covariances between green and red foreground pixels in each spot of each array.

R.bckg

A 45015 x 10 matrix with the means of the red background pixels in each spot of each array.

G.bckg

A 45015 x 10 matrix with the means of the green background pixels in each spot of each array.

R.size

A 45015 x 10 matrix with the number of red foreground pixels in each spot of each array.

G.size

A 45015 x 10 matrix with the number of green foreground pixels in each spot of each array.

array.ids

A vector with the ids for the 10 arrays.

gene.ids

A vector with the ids for the 45015 spots.

gene.names

A vector with the names of the 45015 genes.

Details

It contains data from 10 two-color microarrays, being 5 from tissues representing type II intestinal metaplasia and 5 from tissues representing the normal condition, obtained from the Tumor Bank at A.C. Camargo Cancer Center / Antonio Prudente Foundation.

Each sample is hybridized against a pool of normal tissues using the same orientation of dye labeling. Gene expression levels were measured on Agilent Whole Human Genome Microarrays 4x44K G4112F (design ID 014850).

Each slide contais 45015 spots (41093 unique probes) and each spot contains about 60 foreground pixels.

The scanned images of the microarray slides were processed by Agilent Feature Extraction software, version 9.5, where statistics (mean, standard deviation and covariance) of the foreground and local background pixels were computed for each spot, in both test and reference channels.

The experiment was conducted with financial support of the Foundation for Research Support of the State of S<c3><a3>o Paulo (FAPESP), grant 06/03227-2, and in accordance with the recommendations of the international guidelines for investigations involving human beings with written informed consent from all subjects. The protocol was approved by the Ethics Institutional Committee of the A.C. Camargo Cancer Center (process number 1023/07).

References

\insertAllCited

adele/omicsMA documentation built on May 24, 2019, 1:32 a.m.