Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies.

ABSTRACT:

Background

The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. Spiked-in cRNAs with known concentration are often used to assess the relative performance of probe set algorithms. Given the fact that the spiked-in cRNAs do not represent endogenously expressed genes in experiments, it becomes increasingly important to have methods to study whether a particular probe set algorithm is more appropriate for a specific dataset, without using such external reference data.

Results

We propose the use of the probe set redundancy feature for evaluating the performance of probe set algorithms, and have presented three approaches for analyzing data variance and result bias using two sample t-test sta

SUBMITTER: Hu Z 

PROVIDER: S-EPMC1361777 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature