Commonly used Software:
CONSULTATION ON EXPERIMENTAL DESIGN: no charge
For investigators interested in starting a protein differential expression project, we offer a free initial consultation on experimental design and identification of potential analysis issues. Any further additional data analysis is charged per hour. Investigators are not obligated to get any additional analysis services.
Data analysis includes:
Quality control and Pre-processing: We will use a variety of appropriate methods to assess the quality of individual samples and detect any outliers. Data pre-processing steps, filtering, normalization and imputation will be assessed and implemented if warranted. A data matrix of the final normalized expression values will be provided as well as summary plots to indicate problematic samples.
Differential Expression Testing: We will implement T test ANOVA-based models to test for differentially-expressed proteins. For all comparisons specified by the investigator, a data file will be produced including fold-change, False Discovery Rate-adjusted p-values and any readily-available annotation information.
Results include identification of the proteins in each sample with expression patterns and annotation information, replicates correlation analysis, PCA, Volcano plot, heatmaps of the expression pattern between samples .Other data analysis such as GO enrichment methods are available upon request.