[BioC] Nimblegen and Ringo package

[Todd Richmond]

> -----Original Message-----
> From: João Fadista [mailto:Joao.Fadista at agrsci.dk]
> Sent: Thursday, August 16, 2007 9:49 AM
> To: Todd Richmond; bioconductor at stat.math.ethz.ch; toedling at ebi.ac.uk
> Subject: RE: [BioC] Nimblegen and Ringo package
>
> I am analysing the demo Nimblegen CGH data with Ringo package because I
> think is the only bioconductor package that can convert the .pair raw
> files from nimblegen into RGList, right? After I get the RGList then I can
> use the packages suitable for CGH analysis.

Steven McKinney posted some scripts to get NimbleGen data into snapCGH awhile ago (do a search for NimbleGen + snapCGH). snapCGH will then give you access to at least 3 different algorithms.


> By the way, I came up with another question. As I read through the CGH
> NimbleScan User´s Guide I didn´t find a file that describes the statistics
> of the fluorescent spots for each probe, like the GenePix software does
> (SD of the pixel intensity, Signal to noise ratio, a score for each spot,
> etc.). Can you generate that kind of files?
>

NimbleScan can generate a feature report, which has the mean and SD of the pixel intensities comprising the feature, but that's about it. Our features are only 3x3 pixels, in a checkerboard arrangement, so there's not really enough real estate surrounding each feature to get a reasonable estimate of local background.


> If not, is it possible to transform a .ndf into a .gal file
> (http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.ht
> ml#gal) in order to be able  to analyse the nimblegen .tiff images in
> GenePix?

It's possible to use GenePix 6.0 to extract the .tif images, since it does support square features and rectangular positioning. But when I've tried that, it appears to only quantify a 2x2 pixel feature with no background information - probably due to the close packing of the features. You might be able to make a custom .gal file which would only quantify the "on" positions of the checkboard, thus letting GenePix make some background calculation. But we have no tools to convert a .ndf file to a .gal file...

Regards,
Todd



--
Todd Richmond
NimbleGen Systems, Inc.
Manager of Research Informatics
One Science Court
Madison, WI 53711
1-608-218-7600