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@rd.nestle.com

 


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