How to compare gene TPM values of two different conditions obtained from different experiments (for overview)
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7 months ago

I want to compare gene expression, in the way Gepia tool does by using log2(TPM) values. I have a condition which I would like to compare for a specific gene or set of genes with normal tissue expression (GTEx). I am thinking of comparing the log2(TPM+1) expression of normal tissue expression obtained from GTEx with the dataset I have. I don't have a normal expression dataset from my experiment. Is there something else that can be done such as Z-score (sample size~ 700(GTEx) vs ~22)? Or this approach is ok for the comparison?

PS. it is not a Differential expression analysis (motive is to take some idea, what is happening so that I can plan the next step of my study),

RNA-Seq TPM normalization • 548 views
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Entering edit mode
7 months ago
ATpoint 48k

Or this approach is ok for the comparison?

It is not robust as you do not know whether differences you see are technical or biological. But if this is the only source of data you have then there is not much choice, right?. If possible see whether there are other data sources to at least get some confirmation that any "trend" you derive from the data holds true.

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Thanks for your point. Do you think, a comparison of the house-keeping genes expression between GTEx and data I have, could give me some hints about the different present because of technical artifacts?

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