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RNAseq: units (TPM +0.001).

Excuse me, I have some questions,

If I have units (TPM +0.001), who is taken as 0 or 1 as the cut-off point.

I am analyzing the expression of a gene (normal vs cancer). But I have very negative values ​​with the units (TPM +0.001). I don't know if the 1 or 0 reference should be taken. How should it be interpreted? Can you guide me, please. Thank you

tpm arnseq
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updated by always_learning always_learning • written by alexia.260883 • alexia.260883

Excuse me

You are excused - do not worry.

Can you let us know which data you have retrieved? If you have negative values, then, perhaps, the data that you have is, in fact, log2(TPM + 0.001) or log(TPM + 0.001). It will greatly help us to know the source of this data, though.

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written by Kevin Blighe Kevin Blighe

Thanks. It then makes sense that there are negative values. for example, if TPM = 0, then:

tpm <- 0
log2(tpm + 0.001)
[1] -9.965784

What would you like to do with this data? Can you describe further the files that you have retrieved?

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written by Kevin Blighe Kevin Blighe

I want to compare the expression level of mRNA isoforms of a gen, between normal tissue and cancer

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written by alexia.260883 • alexia.260883

I have many tados with this value -9.96, but I don't know if they are zeros

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written by alexia.260883 • alexia.260883

If it says that a .001 pseudocount was added, and the logged value is consistent with taking the log of the pseudocount alone, yes, they were zeros initially.

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written by swbarnes2 swbarnes2

Take the data from a database called XENA, the expression comes in log2 (tpm + 0.001). But I don't know what the cut-off point is to say if the expression increases or decreases. I don't know what it means -9.965784.

Excuse me, I'm a student and I know the subject well.

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written by alexia.260883 • alexia.260883

There is no "cut-off". RNAseq is a relative experiment where you can compare expression between two conditions after accounting for various covariates.

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written by Ram Ram

What you did do finally? I had a similar problem and finally removed all such entries because It was screwing my box plot.

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written by always_learning always_learning

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