mdanderson.org_HNSC_MDA_RPPA_Core

Created By Kyle Ellrott kellrott
This archive contains the Level 3 data of 212 HNSC primary solid tumor samples and 50 cell line control samples. The cell line samples are not related to TCGA, but they are printed on all the slides (including those with TCGA samples) to serve as a control for further normalization of the data (e.g. combing two batches). Level 3 data are derived from Level 2 data. The normalization is described as follows: Starting with a level 2 data matrix, median center the data of each protein; From 1), calculate the median value for each sample; subtract the sample medians from 2) from the level 2 data of the corresponding samples. This method has proved to work well. However, the savvy user is encouraged try other normalization methods if she likes. A word about batch effect correction: There may be two or more batches for a certain cancer type, e.g. BRCA, UCEC, etc. We are working on methods of batch effect alleviation that is specific to this platform. currently, if there is more than one batch, the batches are normalized separately and uploaded as is.

freeze: tcga_pancancer_v4
acronym: HNSC
disease: cancer
species: Homo sapiens
fileType: genomicMatrix
platform: MDA_RPPA_Core
dataCenter: mdanderson.org
lastUpdate: 2012-08-08
tissueType: head and neck
dataSubType: RPPA
lastUpdated: 2012-08-08