gastro: Gastro-esophagic dataset

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

This dataset is composed of five objects of classes maigesPreRaw, maigesRaw and maiges containing a piece of the dataset that was analysed by the MAIGES (http://www.maiges.org/) and published at Cancer Research (see the reference below). In this dataset we evaluated the profiles of expression for 72 gastro-esophagical samples. Were used cDNA microarrays with slides containing 4800 spots representing approximately 4400 unique genes. The original dataset was composed from 86 samples with dye swap (what makes 172 chips). The dataset available here contain a subgroup of 20 samples (40 chips) and 500 spots (486 unique genes).

The objects available are: - gastro: maigesPreRaw class containing the raw dataset. - gastro.raw: maigesRaw class containing the dataset ready for filtration and normalization. - gastro.raw2: same to the above, after filtration. - gastro.norm: maiges containing the normalized data. - gastro.summ: same to the above, after summary of replicates.

Usage

data(gastro)

References

Gomes, L.I.; Esteves, G.H.; Carvalho, A.F.; Cristo, E.B.; Hirata Jr., R.; Martins, W.K.; Marques, S.M.; Camargo, L.P.; Brentani, H.; Pelosof, A.; Zitron, C.; Sallum, R.A.; Montagnini, A.; Soares, F.A.; Neves, E.J. & Reis, L.F. Expression Profile of Malignant and Nonmalignant Lesions of Esophagus and Stomach: Differential Activity of Functional Modules Related to Inflammation and Lipid Metabolism, Cancer Research, 65, 7127-7136, 2005 (http://cancerres.aacrjournals.org/cgi/content/abstract/65/16/7127)

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.