clippda

The clippda package in R is a software tool that calculates sample size for cancer clinical proteomics studies using MALDI and SELDI profiling. These studies aim to identify biomarkers for early-stage disease by analyzing protein expression data from different clinically defined groups.

Key features of clippda:

1. It accommodates covariate information, data imbalances, and design characteristics such as technical replication and the studies' observational nature.

2. Assumes knowledge of a joint distribution for protein expression values and covariates.

3. Incorporates the effect of discretized covariates by considering the proportions of subjects with specific attributes.

4. Allows for the specification and adjustment of expected heterogeneities, even when pilot data on subject covariates is unavailable.

5. Suggest experimental designs that lead to using fewer samples when planning a study.

An analysis of colorectal cancer proteomic profiling data using clippda revealed that fewer samples are needed when a study is balanced compared to when it is unbalanced, and when the IMAC30 chip-type is used.