
The NimbleGen image analysis software can output the results to 
different formats (pairs, xys, ...), all containing slightly different 
information for a given hybridization. The NDF is the most complete 
description for the probes on a given array, and there is no need to 
repeat that information in all pairs/xys/whatever files.

Regarding the meaning of the categories, the types can vary from array 
to array. NGS_CONTROLS can be internal controls for placing the grid 
during image analysis. You can mostly make sense of them by looking at 
the corresponding text in the other columns (DESIGN_NOTE for example).
**
Otherwise, this is not directly related to bioconductor and may be the 
NimbleGen technical support would answer this better ?


L.

On 01/12/10 06:00, Dario Strbenac wrote:
> Hello,
>
> I've been looking at the NDF of a certain chip (2007-09-21_MM8_Deluxe_Promoter_HX1.ndf) and the pair files. I've noticed that in the NDF there are 5 types of probes - "BLOCK1"       "H_CODE"       "NGS_CONTROLS" "RANDOM"       "V_CODE". But in the pair files, there is just "BLOCK1" and "RANDOM". Why are the other 3 types not in the results ? Also does anyone know what the categories actually mean ? There isn't any explanation in the official document that comes with the arrays from the manufacturer (NimbleGen_Data_Formats_v2p1.pdf) or online.
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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