Glossary

Raw counts	Raw counts are the direct output from a pipeline, obtained after trimming, demultiplexing, alignment, and mapping. Raw count values generally are whole numbers and will not contain decimals.
Normalized counts	Raw counts that are normalized by accounting for gene length, sequencing depth, or expression distribution.
False discovery rate (FDR), q value, adjusted P value	These terms describe the same concept, namely a P value that has been adjusted to account for multiple hypothesis testing.
PCA	Principal component analysis (PCA) reduces data dimensionality and describes variation using principal components (PCs).
Benjamini-Hochberg (BH) adjustment	A method of calculating the FDR by limiting the expected ratio of false-positive results, or type I errors, in the results. The adjustment is calculated by ranking P values, calculating individual BH values, and comparing the BH values with P values.
RPKM	Reads per kilobases of transcript per 1 million mapped reads. RPKM is calculated as follows: [number of mapped reads]/[(transcript length/1,000)/(total reads)/106)].
FPKM	Fragments per kilobases of transcript per 1 million mapped reads. FPKM is calculated as follows: [number of fragments]/[(transcript length/1,000)/(total reads)/106)].
CPM	Counts per million. CPM does not account for gene or transcript length.