[BioC] package charm, creating .xys files

[Benilton Carvalho]

Hi Johnny,

1) The SIGNAL is the PM column;

2) About the controls... Look at the NDF file... All the PMs are
*expected* to have PROBE_CLASS == 'experimental' and MISMATCH == 0
(you can double check this[*])... then, everything else is
'control'... A shortcut that might work (never tried) is get get all
the X/Y coordinates for which you don't have readings on the PM column
of your .pair file.

3) Yes.

4) After having the 3 required columns for the XYS, remember to sort
the rows so you have something like:

X   Y   SIGNAL   COUNT
1   1   <value_or_NA>  <value_or_NA>
1   2   <value_or_NA>  <value_or_NA>
1   3   <value_or_NA>  <value_or_NA>
......
2   1   <value_or_NA>  <value_or_NA>
2   2   <value_or_NA>  <value_or_NA>
etc

(download the maqcExpression4plex package and check the XYS files in
its 'extdata' directory for reference)

HTH,

b

On 27 January 2012 20:46, Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis
Petcare <Qinghong.Li at rd.nestle.com> wrote:
> Hi,
>
>
>
> I am trying to create an annotation package so I can use  "charm" to
> analyze nimblegen rat data. We have only .pair files but the .tiff
> files. So won't be able to generate the .xys files using NimbleScan.
>
>
>
> I have a few questions:
>
> 1.       what does the SIGNAL column in .xys file come from? Is it the
> PM column in the .pair file?
>
> 2.       I was told all control probes have NAs in both SIGNAL and
> COUNT, how do I know which ones are control?
>
> 3.       I assume X Y columns are the same in both pair and xys files?
>
>
>
> Here is the old threat on similar topic:
> http://answerpot.com/showthread.php?662032-XYS+from+nimblegen
>
>
>
> Thanks,
>
> Johnny
>
>
>
>
>
>
>
>
>
>
>
>
>
> ******
>
> Johnny Li, Ph.D.
>
> Nestle Purina PetCare Company
>
> Saint Louis, MO 63164
>
>
>
> Tel: (314) 982-2295
>
> Fax: (314) 982-5857
>
> Email: qinghong.li at rd.nestle.com
>
>
>
>
>        [[alternative HTML version deleted]]
>
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