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Analyzing dataset with counts and TMM values?

Hello! To preface, I am a total beginner to bioinformatics.

I am analyzing a dataset of Alzheimer's disease for my project. The dataset contains a number of genes and their counts and TMM values across 6 different samples.

I have analyzed a different dataset containing genes and their logFC values to determine the upregulated and downregulated genes, so I have some idea how to analyze datasets like that, but this is the first time I'm encountering TMM values and I'm a little unsure how to go about analyzing gene expression levels (or if that is the next step at all). I would really appreciate any tips, resources, tutorials, etc. Thank you so much!

tmm counts gene-expression
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written by trkfs • trkfs

1 answer

Hey trkfs,

I assume you are talking about bulk RNAseq samples? In this case, I recommand you take a look at the extremely useful and comprehensive DESeq2 vignette. This will give you an idea how to get from counts to a table which contains differentially expressed genes. Alternatively, you can also use edgeR. A useful pointer for this, would be this paper.

On a side note, TMM values are very useful for visualizing the expression differences between samples for a given gene. However, if you are interested in identifiying differentially expressed genes (which is almost always the case) all state-of-the-art tools/methods use raw counts.

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written by nhaus • nhaus

Hi nhaus, yes the dataset is RNAseq samples. And thank you so much for your answer! Really grateful for the resources you've provided and your explanations. Helped clear up my confusion :)

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written by trkfs • trkfs

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