lincs_expr: LINCS Intensity Signature Database

In yduan004/signatureSearchData: Datasets for signatureSearch package

LINCS Intensity Signature Database

Description

The LINCS Level 3 data can be downloaded from GEO the same way as described for the Level 5 data available at help file of lincs. The Level 3 data contain normalized gene expression values across all treatments and cell lines used by LINCS. The Level 3 signatures were filtered using the same dosage and duration criteria as the Level 5 data. The biological replicate information included in the Level 3 data were collapsed to mean values. Subsequently, the resulting matrix of mean expression values was written to an HDF5 file. The latter is referred to as lincs_expr database containing 38,824 signatures for a total of 5,925 small molecule treatments and 30 cell lines. Although the LINCS Level 3 and 5 data are filtered here the same way, the number of small molecules represented in the Level 3 data (5,925) is smaller than in the Level 5 data (8,140). The reason for this inconsistency is most likely that the Level 3 dataset, downloadable from GEO, is incomplete.

Details

The filtered and processed LINCS Level3 data (lincs_expr) can be loaded from Bioconductor’s ExperimentHub interface as shown in Examples section. In this case the loaded lincs_expr instance includes mean expression values of 12,328 genes for 5,925 compound treatments across a total of 30 cell lines (38,824 signatures in total). This data set can be used by all correlation-based GESS methods provided by the signatureSearch package.

The loaded lincs_expr data object is filtered and generated from the original LINCS level 3 data stored at GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742. For documentation and code of generating the lincs_expr databases from sources, please refer to the vignette of this package by running browseVignettes("signatureSearchData") in R.

References

LINCS source data at 5 levels from GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742

Examples

library(ExperimentHub)
# eh <- ExperimentHub()
# query(eh, c("signatureSearchData", "lincs_expr"))
# lincs_expr_path <- eh[["EH3227"]]
# rhdf5::h5ls(lincs_expr_path) 

yduan004/signatureSearchData documentation built on April 7, 2023, 4:12 a.m.