Hello,
I have one basic question, I would like to know the relationship between Log2 Fold change and Log2 TPM in RNA-seq data. Specifically, One particular gene A Log2 TPM is 9 and its Log2 Foldchange 3 fold. I am not able to understand how this gene TPM is higher and foldchange is low comparatively. Can anybody explain?
Thanks, Ni
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saigro16 •
TPM (Transcripts Per Million) refers to how much RNA is present in a sample. For example, a Log2 TPM of 9 means that for every million transcripts in your sample, 2^9 of them are from gene A. It is the expression level of gene A in a sample.
Log2Foldchange describes how one sample is different from another. In this case it is saying that the expression level in Condition 2 is 8 (2^3) times as high as it is in Condition 1.
So if the log2 expression level in condition 1 is 9 TPM, and there is a log2foldchange of 3 between condition 1 and condition 2, then the log2 expression level in condition 2 will be 12 TPM (2^9 * 2^3).
Thank for the clear explanation, I have one more question how should we explain when log2TPM of a particular gene is around 5 and its log2 foldchange is -1.15?
Thank you for the reply, regarding Log2 foldchange -1.15 I got it but I am not able to understand how does it relate to Log2 TPM is in positive value 5.
It doesn't relate to this.
A gene cannot have one log2TPM in two conditions, nor a log2 fold change in two conditions.
If you have two condidtions, you have two different values from log2TPM, one in each condition.
If, for example your log2 TPM is 5 in the control condition, and the log2Fold change between control and treatment is -1.15, then the expression level in the treatment condition would be 3.85.
Excellent explanation, thank you. One small typo 2^3 = 8 not 6.
log2(TPM) is simply the log2 of the Transcript Count Per Million. TPM is a normalization technique (but not a good one) to scale the read count per gene/transcript towards the total read count of the sequencing run in order to compensate for different sequencing depths. See this video for details. The Log2FC is a measure of how much the expression of a gene changes between two conditions.
what would be an example of a better measure than TPM?
Don't compare these two units - its not apples to apples comparison. TMP is a unit of expression. Fold Change is a unit showing how much TPM has changed in one condition compared to another condition.
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