Supplementary Material: Proximity Measures for Clustering Gene Expression Microarray Data: a Validation Methodology and a Comparative Analysis
Creators: name: Andretta Jaskowiak, Pablo
name: Campello, Ricardo
name: Gesteira Costa, Ivan
Publisher: name: Zenodo
Year: 2013
Subjects: Clustering
Cluster Analysis
Gene Expression

description: <strong>This is the Supplementary Material for the paper: </strong> P. A. Jaskowiak, R. J. G. B. Campello and I. G. Costa, "Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis," in <em>IEEE/ACM Transactions on Computational Biology and Bioinformatics</em>, vol. 10, no. 4, pp. 845-857, July-Aug. 2013, doi: 10.1109/TCBB.2013.9. We provide a file with supplementary results and two sets of benchmark data, proposed in the paper. Regarding datasets, there are two main sets of data, as described below. <strong>Original Data – Results shown in our paper</strong> The collection of 17 datasets that we propose as benchmark in our paper. Note that these datasets are publicly available from their original sources. In this version, however, we selected about 1000 genes in each dataset, which were analyzed. In the zip file you will find 17 csv files, one for each dataset. (datasets are named following Table 2 from our paper). The files are in the following format: First row: file header containing, in this sequence: Gene number in the original dataset. Gene identifier (name). Times (in minutes) at which expression values were measured for each gene. The remainder of the file contains gene expression values for each gene. Additionally, in the same zip file, we provide a file called fold_change.xls. In this file we detail the values of l and c that were employed during the filtering stage (fold change). This procedure was employed in order to select about 1000 genes for each dataset. For original sources for each dataset, please refer to Table 2 from our paper. <strong>Normalized Data – Results shown in our supplementary pdf file</strong> Following suggestion from one of the reviewers we also performed experiments on normalized versions of the aforementioned datasets. Since we were unable to locate the original array files for one of the datasets, experiments were performed on 16 datasets. Results for these experiments are available on our pdf supplementary file. We also compiled these datasets. These were normalized with Multiple-Slide Normalization. We also selected about 1000 genes for each dataset employing fold change. In the zip file you will find 16 csv files, one for each dataset. For further information on normalization of such datasets, please, refer to our pdf supplement. The name of each dataset follow the same convention previously adopted. Files are in the following format: First row: file header containing, in this sequence: Gene identifier (name). Times (in minutes) at which expression values were measured for each gene. The remainder of the file contains gene expression values for each gene. Additionally, in the same zip file, we provide a file called fold_change.xls. In this file we detail the values of l and c that were employed during the filtering stage (fold change). This procedure was employed in order to select about 1000 genes for each dataset. For original sources for each dataset, please refer to Table 2 from our paper.
description: {"references": ["P. A. Jaskowiak, R. J. G. B. Campello and I. G. Costa, \"Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis,\" in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 4, pp. 845-857, July-Aug. 2013, doi: 10.1109/TCBB.2013.9."]}