[BioC] FW: limma for 2 color data

[Sean Davis]

On Tue, Apr 15, 2008 at 8:26 AM, Afsaneh <s.maleki-dizaji at dcs.shef.ac.uk> wrote:
> Thanks, but the problem is how to order and also do you know how can I replace NA  (missing value) with 0 or delete them.

Afsaneh,

It is best to reply to the list so that everyone can benefit from your
questions.

See the order() function for ordering.  I would simply ignore the NAs,
as they will be placed "last" by order.  Again, see the help for
order() for more details.

Sean


>
>  -----Original Message-----
>  From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis
>  Sent: 15 April 2008 13:12
>  To: Afsaneh
>  Cc: bioconductor at stat.math.ethz.ch
>  Subject: Re: [BioC] FW: limma for 2 color data
>
>  On Tue, Apr 15, 2008 at 8:03 AM, Afsaneh <s.maleki-dizaji at dcs.shef.ac.uk> wrote:
>  > Dear Sean,
>  >  Thanks for reply but when I try,
>  >  > topTable(MA,sort.by='M')
>  >
>  > Error in dim(data) <- dim : attempt to set an attribute on NULL
>
>  topTable() will not work on an MAList.
>
>  >  I get error, so how can I get top 10 expressed genes.
>
>  You can take the ratio of red/green (or green/red) and order those
>  ratios from greatest to least.
>
>  Sean
>
>