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Series GSE9309 Query DataSets for GSE9309
Status Public on Oct 20, 2007
Title Recovery of biological information under heterogeneous experimental conditions using subgroup standardization.
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Recovery of biological information (i.e. Breast tumor versus non-tumor part of breast) from microarray data under heterogeneous experimental conditions (Buffer1 versus Buffer2) using subgroup standardization.
Microarray is a useful tool for gene expression analysis and prediction. For a given disease, a microarray database may come from various sources with different experimental setups, collected over time. This heterogeneity provides unnecessary complication in data analysis and, even worse, given false classification in clustering. Therefore, it is practically important to provide a standard data treatment for microarray data from heterogeneous experimental conditions. In this work, “subgroup standardization” is proposed to compensate technical heterogeneities (e.g., buffers, time, machines etc.) in microarray experimental conditions. Provided with repetitive microarray experiments, over time and buffers, the results indicate that the proposed approach can extract correct biological information in the presence of technical irregularities. Hierarchical clustering is used to validate the effectiveness of the proposed approach.
Keywords: disease state study
Overall design 98 of breast cancer specimens and 8 of non-tumor part of breast specimens were applied in the study. All the signals from the mRNA profile of each sample in the microarrays were normalized using the internal control RNA- Stratagene's human common reference RNA.
Contributor(s) Yao HC, Mudi RK, Yu CC, Juan HF, Chen HW, Hsieh FJ, Chang LY, Hwa HL, Kuo WH, Chang KJ, Lin YS
Citation(s) 23516564
Submission date Oct 12, 2007
Last update date Oct 28, 2019
Contact name Hsin-Chieh Yao
Organization name National Taiwan University
Department CHE
Street address 1, Rd. Roosevelt, Sec. 4
City Taipei
ZIP/Postal code 106
Country Taiwan
Platforms (1)
GPL887 Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)
Samples (142)
GSM237137 breast tumor part_IDC_rep1_1257
GSM237138 breast tumor part_ILC_rep1_1259
GSM237139 breast tumor part_IDC_rep1_1261
BioProject PRJNA102963

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9309_RAW.tar 623.9 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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