Tbtools Expression Calculate Rpkm Fpkm Tpm

TPM Equation:

\[ TPM = \frac{FPKM \times \text{Effective Length}}{\sum(FPKM \times \text{Effective Length})} \times 10^6 \]

TPM Value:

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1. What Is TPM?

TPM (Transcripts Per Million) is a normalized unit for measuring gene expression levels in RNA-seq data. It accounts for both gene length and sequencing depth, providing a more accurate comparison of expression levels across different genes and samples.

2. How Does The Calculator Work?

The calculator uses the TPM equation:

\[ TPM = \frac{FPKM \times \text{Effective Length}}{\sum(FPKM \times \text{Effective Length})} \times 10^6 \]

Where:

\( FPKM \) — Fragments Per Kilobase Million
\( \text{Effective Length} \) — Effective gene length in base pairs
\( \sum(FPKM \times \text{Effective Length}) \) — Sum of all FPKM × Effective Length products

Explanation: TPM normalizes expression data by scaling the sum of all TPM values to 1 million, allowing direct comparison between samples.

3. Importance Of TPM Calculation

Details: TPM provides a standardized measure of gene expression that is comparable across different experiments and sequencing platforms. It's widely used in transcriptomics research for differential expression analysis.

4. Using The Calculator

Tips: Enter FPKM value, effective gene length in base pairs, and the sum of all FPKM × Effective Length products. All values must be positive numbers.

5. Frequently Asked Questions (FAQ)

Q1: What's the difference between TPM and FPKM?
A: While both normalize for gene length and sequencing depth, TPM scales the sum of expression values to 1 million, making it more suitable for sample comparison than FPKM.

Q2: When should I use TPM instead of FPKM?
A: TPM is generally preferred for comparing expression levels across different samples, while FPKM is better for within-sample comparisons.

Q3: How do I calculate the sum product?
A: The sum product is calculated by summing the product of FPKM and effective length for all genes/transcripts in your dataset.

Q4: What is effective length?
A: Effective length accounts for the fact that reads can map to multiple positions and is typically slightly shorter than the actual transcript length.

Q5: Can TPM values be compared between different studies?
A: While TPM provides better normalization, caution should still be exercised when comparing across different studies due to variations in experimental protocols.