Scaling Land FPKM values to TPM

From Array Suite Wiki

Revision as of 11:00, 28 September 2018 by Joseph (Talk | contribs)
Jump to: navigation, search

Contents

Enabling TPM-scaling of Land FPKM Values in OmicSoft Lands

UseTPM.png

Overview

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.

DontUseTPM.png

FPKMScaledExpression.png

UseTPM.png

TPMScaledExpression.png


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.

Supported Views

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".

Related Pages

EnvelopeLarge2.png