Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?

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15 months ago

JLee • 0

Hi!

I downloaded a differential gene expression summary data table like this from brainSCOPE.

enter image description here

All I need are the gene and log2FoldChange column. However, each gene's data is split into multiple different cell types, as indicated in the cell_type column. These are too many cell types to work with- so I just want to merge some cell subtypes into larger cell types- e.g., I want to merge Vip, Sst, Pvalb cells into just "interneuron".

In this case, can I simply get the mean of log2FoldChange values of Vip, Sst, Pvalb for each gene? I don't care about p-values because I will analyze log2FC values with threshold-agnostic methods.

scrna-seq rna-seq log2fc • 609 views

ADD COMMENT • link 15 months ago by JLee • 0

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logFCs without stats are meaningless since logFCs can have large standard errors. Combining individual logFCs can introduce bias as high logFCs with large SEs can overwrite reliable but moderate logFCs, I don't see the point. If the data format does not allow your analysis then get the underlying data and analyse as needed.