[R] Comparing two groups of proportions

[Ivan Adzhubey]

Hi,

I have a seemingly common problem but I can't find a proper way to approach 
it. Let's say we have 5 samples (different size) of IC circuits coming from 5 
production lines (A, B, C, D, E). We apply two different non-destructive QA 
procedures to each sample, producing to sets of binary outcomes (passed: 
no/yes). So, we have two groups of proportions:

	QA1		QA2
	no/yes	no/yes
A	10/90	8/92
B	5/15		7/13
C	1/79		2/78
D	12/38	10/40
E	3/7		1/9

How would I test if the two QA procedures in question give significantly 
different results, at the same time controlling for the possible production 
line contribution? It looks like there are many variants of multiple 
proportions tests available in R and various extra packages but none seems to 
exactly fit this very simple problem. I would appreciate any advice.

Thanks,
Ivan

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