Influence of batch effect correction methods on drug induced differential gene expression profiles.

ABSTRACT:

Background

Batch effects were not accounted for in most of the studies of computational drug repositioning based on gene expression signatures. It is unknown how batch effect removal methods impact the results of signature-based drug repositioning. Herein, we conducted differential analyses on the Connectivity Map (CMAP) database using several batch effect correction methods to evaluate the influence of batch effect correction methods on computational drug repositioning using microarray data and compare several batch effect correction methods.

Results

Differences in average signature size were observed with different methods applied. The gene signatures identified by the Latent Effect Adjustment after Primary Projection (LEAPP) method and the methods fitted with Linear Model

SUBMITTER: Zhou W 

PROVIDER: S-EPMC6706913 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature