[GeneX-dev] Re: Genex

[Harry M. <man...@ho...>]

Ratio data is ... ratio data.  data that consists of ratios between the cy3 and cy5 values.  If you have the data you describe below, you'll have to create ratios out of it which is trivial in a
spreadsheet or via a perloid.

you need a format that looks like:

gene1 cy3/cy5  cy3/cy5  cy3/cy5
gene1 cy3/cy5  cy3/cy5  cy3/cy5
gene1 cy3/cy5  cy3/cy5  cy3/cy5
gene2 cy3/cy5  cy3/cy5  cy3/cy5
gene2 cy3/cy5  cy3/cy5  cy3/cy5
gene2 cy3/cy5  cy3/cy5  cy3/cy5

where 'cy3/cy5' is a floating point ratio which is the result of dividing the cy3 value by the cy5 value.  In the above case, there would be 3 replicates.

hjm

Yue Wang wrote:
> 
> Dear Harry:
> 
> I have installed the Genex in my workstation. I try to
> learn how to use them. For cyberT part I can't
> understand what mean ratio data, label columns and
> Minimum non-zero Replicates Required. I read the
> documentation I still don't know how to fill them.
> Suppose I have a mircoarray data set as following:
> 
> gene1 cy3 cy5  cy3 cy5  cy3 cy5
> gene1 cy3 cy5  cy3 cy5  cy3 cy5
> gene1 cy3 cy5  cy3 cy5  cy3 cy5
> gene2 cy3 cy5  cy3 cy5  cy3 cy5
> gene2 cy3 cy5  cy3 cy5  cy3 cy5
> gene2 cy3 cy5  cy3 cy5  cy3 cy5
> 
> So how to fill the "ratio data"? Do i need calculate
> ratio cy3/ cy5 first, save them and give them label,
> then fill the blank? For the replicate is it 3? Is the
> format right for the above example?
> 
> Thanks.
> 
> Yue

-- 
Cheers, Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... 
                    [plain text appreciated]