Welcome to PLIER: Pathway-Level Information ExtractoR. All you need to use PLIER is a gene expression matrix. The requirements are:

• Tab separated with column and row names
• Use human gene symbols (HGNC Gene Symbol or Ensembl ID) for built-in prior information sources
• Data should be log transformed and normalized with you preferred normalization method (for example quantile normalization)
• The data will be z-scored internally so it doesn't matter whether it is microarray intensities or RNAseq FPKM, TPM, or counts as long as it is log transformed

The data should look like as follows. PLIER can not run with too few samples (<=3). The sample size should be large enough (>10 is preferred).

	Sample1	Sample2	Sample3
ACTB	1	2	3
TP35	4	5	6
EGFR	7	8	9