RT Journal Article
SR Electronic
T1 l1kdeconv: an R package for peak calling analysis with LINCS L1000 data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 165258
DO 10.1101/165258
A1 Zhao Li
A1 Jin Li
A1 Peng Yu
YR 2017
UL http://biorxiv.org/content/early/2017/07/18/165258.abstract
AB Background 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.Results 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.Conclusions 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.Contact pengyu.bio{at}gmail.com