Subsampling with CLR

Theory behind mothur
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Hi there,

I’m wanting to use CLR transformed OTU data for differential abundance analysis.

Should I be feeding the make.clr command the raw shared file, or the subsampled shared file?

Thanks,

Lisa.

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Hi Lisa,

Welllll… CLR is supposed to be insensitive to sampling effort so I’d say use the raw shared file. But, I’ve seen that it is actually quite sensitive to sampling effort. I’m not sure that CLR makes sense on subsampled data. I should have a preprint up by the end of the month on this. But for now, you can check out this video…

Pat

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