Significance analysis of microarray for relative quantitation of LC/MS data in proteomics

doi:10.1186/1471-2105-9-187

BMC Bioinformatics

Volume 9

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Methodology article

Significance analysis of microarray for relative quantitation of LC/MS data in proteomics

Bryan AP Roxas¹ and Qingbo Li¹^,2

¹Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA

²Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60607, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:187doi:10.1186/1471-2105-9-187


Published:	10 April 2008

Additional files

Additional file 1:

Table 2 – Protein and peptide data for statistical significance analysis. The table shows the protein relative abundance, standard deviation (SD), number of unique peptides (#Pep) and number of PCS's (#PCS) for each protein in the sample replicates pH5A, pH5B, pH5C, pH7A, pH7B, pH7C, pH5p, and pH7p. Results of the fold change test, the 2 t-tests, and the SAM analysis are shown to the right of the table. The '-' sign indicates missing value (for abundance data) or insignificant change (for statistical testing). The table is in Microsoft Excel format.

Format: XLS Size: 184KB Download file

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Additional file 2:

Table 3 – Comparison of the SAM outputs with the conventional t-test results. The first column contains the locus numbers for the locus names http://www.tigr.org webcite with the prefix 'MSMEG' omitted for brevity. d – observed score in SAM. fc – fold change. '-' – not significant. This table is a condensed version of Table 2 showing only the regulated proteins and their statistical testing results. The table is in PDF format.

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