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Answer: discrepancy in IDs from file and tx2gene (IDs don't match) by James W. MacDonald 68k

I don't think there's an easy fix (depending on your definition of easy, which may vary from mine). Ideally the transcript IDs used for ali…

Answer: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by Aaron Lun ★ 28k

Consider using a `SVT_SparseMatrix` from the **SparseArray** package, which is explicitly designed for this. **DropletUtils** (in BioC-deve…

Comment: Regarding the issue of background genes in enrichment analysis by zalinkaelisa • 0

Use good features to distinguish the situation of the type of experiment [baseball 9][1] [1]: https://baseball9.io/

Comment: Heatmap of the Count Matrix by gta5movilecom • 0

Using it for the top 20 genes in the heatmap highlights high-expression genes, but may miss out on variance-driven patterns. If you want to…

Answer: Regarding the issue of background genes in enrichment analysis by ATpoint ★ 4.9k

It should imo be the genes that were eligable to yield a "significant" result in your analysis. So, if you test set is derived from differe…

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