Question

How many arrays are "enough" for creating useful fRMA vectors?

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Tim Triche ★ 4.2k

@tim-triche-3561

Last seen 3.6 years ago

United States

Hi all,

I'm remapping a bunch of hgu133plus2 probes to novel transcripts. It seems like I need to redefine a number of probesets to do this properly, which is not a big deal, but I also want to use fRMA on the resulting data structure. I have about 1000 CEL files from roughly comparable tissues lying around. Is that enough to reliably generate new and usable frma vectors?

Thanks!

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ADD COMMENT • link updated 9.4 years ago by Matthew McCall ▴ 830 • written 9.4 years ago by Tim Triche ★ 4.2k

score 0 · Answer 1 · 2014-12-11

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Matthew McCall ▴ 830

@matthew-mccall-4459

Last seen 4.9 years ago

United States

Tim,

I believe your question is answered by Table 1 of this paper:

http://www.biomedcentral.com/1471-2105/12/369

But I would add that it also depends on what you are planning to do with the fRMA vectors. Specifically, I would think about whether your training data captures the type of within- and between-batch variability you are likely to see in the data you are planning to preprocess with these vectors.

Best,

Matt

ADD COMMENT • link 9.4 years ago Matthew McCall ▴ 830

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Well, I don't have any technical replicates between batches, but it looks like 5-10 batches of 100-200 arrays should work well enough. I'm just porting a technique from the Liu lab that I want to mechanize on a few thousand arrays with reproducible results. fRMA/barcoding seems like the easiest way to make it happen. Thanks much! For your reply and for the frmaTools package. I am doing some maintenance myself today so I recognize it is largely thankless. Best, --t > On Dec 11, 2014, at 8:49 AM, "Matthew McCall [bioc]" <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User Matthew McCall wrote Answer: How many arrays are "enough" for creating useful fRMA vectors?: > > Tim, > > I believe your question is answered by Table 1 of this paper: > > http://www.biomedcentral.com/1471-2105/12/369 > > But I would add that it also depends on what you are planning to do with the fRMA vectors. Specifically, I would think about whether your training data captures the type of within- and between-batch variability you are likely to see in the data you are planning to preprocess with these vectors. > > Best, > > Matt > > You may reply via email or visit A: How many arrays are "enough" for creating useful fRMA vectors?

ADD REPLY • link 9.4 years ago Tim Triche ★ 4.2k