Introduction

LINCS L1000 is a high-throughput technology that allows gene expression measurement in a large number of assays. However, to fit the measurements of ~1000 genes in the ~500 color channels of LINCS L1000, every two landmark genes are designed to share a single channel. Thus, a deconvolution step is required to infer the expression values of each gene. Any errors in this step can be propagated adversely to the downstream analyses.We presented a LINCS L1000 data peak calling R package l1kdeconv based on a new outlier detection method and an aggregate Gaussian mixture model (AGMM). Upon the remove of outliers and the borrowing information among similar samples, l1kdeconv showed more stable and better performance than methods commonly used in LINCS L1000 data deconvolution.Based on the benchmark using both simulated data and real data, the l1kdeconv package achieved more stable results than the commonly used LINCS L1000 data deconvolution methods.

Publications

  1. l1kdeconv: an R package for peak calling analysis with LINCS L1000 data.
    Cite this
    Li Z, Li J, Yu P, 2017-07-01 - BMC bioinformatics

Credits

  1. Zhao Li
    Developer

    TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, United States of America

  2. Jin Li
    Developer

    TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, United States of America

  3. Peng Yu
    Investigator

    TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, United States of America

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Summary
AccessionBT002172
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByPeng Yu