基因差異表達之一 - RPKM, FPKM, TPM, 傻傻分不清楚

圖片來源：Robinson M D, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data[J]. Genome biology, 2010, 11(3): R25.

下面PPT來源：RPKM, FPKM and TPM, clearly explained

RPKM （Reads Per Kilobase Million)

FPKM (Fragments Per Kilobase Million)

TPM (Transcripts per million)

Normalized read counts for

• Sequencing depth (the Million part)

Sequencing runs with more depth witll have more reads mapping to each gene.

• The length of the gene (the Kilobase part)

Longer genes will have more reads mapping to them

Example: an imaginary RNA-seq data with three replicates (Rep1, 2 and 3) for a genome with 4 genes (A, B, C and D).

參考資料：

1，RPKM, FPKM and TPM, clearly explained

2，What the FPKM? A review of RNA-Seq expression units

3，In RNA-Seq, 2 != 2: Between-sample normalization

4，RNA-Seq normalization explained

5，https://groups.google.com/forum/#!topic/rsem-users/IaZmviqghJc