Scaling Land FPKM values to TPM
From Array Suite Wiki
Enabling TPM-scaling of Land FPKM Values in OmicSoft Lands
OmicSoft Land RNA-seq data generally are Scaled FPKM values (reads/fragments per kilobase of transcriptome, per million reads mapped). Starting in 2018, certain Lands support the "Use TPM" option, if the user prefers to see TPM (Transcripts per million)-scaled values.
Enabling TPM scaling
If an OmicLand's sample-level metadata contains the column "TPM Scaling Factor", the "Use TPM" option will be available in the "Search Options" arrow. Enabling this will immediately re-scale any open View tabs with supported data, and subsequent searches will be scaled. This option can be turned off at any time to return to FPKM scaling.
If a Land does not support TPM scaling, the option will be greyed-out. If a Land contains some samples with TPM scaling and others without (e.g. Virtual Lands), enabling this option will display only TPM-scalable samples.
All gene-level and transcript-level RNA-seq quantification views can support TPM-scaling. Exon, fusion, and junction quantification Views will not be scaled. Nor will "Integration (Scan all genes)" functions such as RNAseq-RNAseq Dynamic Correlation. The axis labels will be updated if TPM-scaling was enabled.
Calculating the TPM Scaling Factor
The TPM Scaling Factor is calculated for each sample by (1/Sum of all FPKM values). The value is stored in the Sample metadata in "TPM Scaling Factor".
- RNA-seq normalization in OmicLands
- Explanation of TPM and FPKM Scaling
- Normalize RNA-seq analysis FPKM data to TPM