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example data

Francisco García edited this page Mar 27, 2015 · 37 revisions

General

Tutorial

Analysis tools

Worked examples

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Available Data for Examples

Clustering:

Data type: Data matrix, Expression

Class prediction:

Data type: Data matrix, Expression

Single enrichment:

Data type: ID list, Id

Network enrichment:

Data type: ID list, Id

Gene set enrichment and & Gene set network enrichment:

Data type: ID list, Ranked


More example datasets

Here you can download some example datasets to work with different analysis modules in Babelomics. For example, normalized data are the input for pre-processing, clustering, differential expression or class prediction analysis. You can find several raw data of several platforms (Agilent, Affymetrix,...) to try several normalization methods:


1. Human Embryonic Stem Cells Under Hypoxia Conditions

A time course study. 16 Agilent one-color arrays.

  • Raw data: 16 Agilent arrays. Raw data files + sample information are provided in a zip file. (143 MB).
  • Design of experiment
  • Sample information: classification information of each sample (array). In a tab delimited text file.
  • Normalized data: using agilent background correction and quantiles between array normalization. Tab delimited text file. (8.000 genes)

#####2. Peripheral Blood Mononuclear Cells After Maternal Separation Two class comparison using two color microarray with a common reference design. 10 GenePix GPR two color expression arrays from van Heerden et al.

  • Raw data
  • Sample information: classification information of each sample (array). In a tab delimited text file.
  • Normalized data: using these normalizations methods: normexp, printtiploess and quantiles between arrays. Tab delimited text file.

#####3. Rheumatoid Arthritis and Osteoarthritis Study

Three class comparison. 15 Affymetrix expression arrays from two disease conditions and a control. Data taken from GEO GSE1786.

  • Raw data: 15 Affymetrix U133A raw data files (CEL files) + sample information are provided in a zip file. (46 MB).
  • Sample information: array classification in a tab delimited text file.
  • Normalized data: using rma method. Tab delimited text file.

#####4. Gene Expression in Healthy Trained and Sedentary Males


#####5. Apocrine Breast Cancer Tumours


#####6. Pulmonary Sarcoidosis


#####7. Hypophariyngeal cancer

Find the Babelomics suite at http://babelomics.org