Question

How many samples suggested to perform differential gene expression analysis?

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6.7 years ago

John ▴ 270

Hi, I have 64 single cell RNA sequences when I cluster them (supervised clustering using monocle) I get two clusters 6 samples each. Is it enough to perform differential gene expression analysis? Or how many samples suggested?

thanks!

RNA-Seq rna-seq r R • 1.3k views

ADD COMMENT • link updated 6.7 years ago by Nick ▴ 30 • written 6.7 years ago by John ▴ 270

score 1 · Answer 1 · 2018-04-04

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6.7 years ago

Nick ▴ 30

What are you using to perform the analysis? I find that DESeq2 is quite good, even with fewer than 6 samples in each group. Naturally, you will reduce noise the more samples you add so if you find that with 6 samples per group you have >2500 DEGs, adding more samples will help to reduce this number.

ADD COMMENT • link 6.7 years ago by Nick ▴ 30

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I think the poster means he has two clusters of 6 cells each. I don't know if you can put that straight into DESeq2 and get meaningful results.

ADD REPLY • link 6.7 years ago by swbarnes2 14k

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What else I should do swabarnes2 ? I use EBSeq not DESeq.

ADD REPLY • link 6.7 years ago by John ▴ 270

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Hi nick, I use EBSeq, which have me around 2000 upregulated & 3000 downregulated genes with FDR set to 5%. Is that fine?

ADD REPLY • link 6.7 years ago by John ▴ 270