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CICAMS-Liu-lab / ECGEA

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Filtering criteria for mRNA expression matrices #1

Open duyuhui opened 1 year ago

duyuhui commented 1 year ago

I saw in the article that the mRNA expression matrix is filtered according to TMM, while in the code it is filtered by cpm, and the filtering ratio is also different. I would like to know which method you are using. Thank you.

CICAMS-Liu-lab commented 1 year ago

Thank you for your attention.

edgeR was used to perform TMM and CPM normalization for the the gene expression. TMM is first used to normalize the depth of sequencing in different samples and estimate the expression level for each sample , and then CPM is used to normalize the amount of read count expression between samples. Both TMM and CPM were used to normaliz read counts of genes were applied to clustering and compare among samples in the downstream analysis.

At 2023-01-09 11:34:07, "duyuhui" @.***> wrote:

I saw in the article that the mRNA expression matrix is filtered according to TMM, while in the code it is filtered by cpm, and the filtering ratio is also different. I would like to know which method you are using.

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