[BioC] Nimblegen and Ringo package
todd at nimblegen.com
Thu Aug 16 17:27:08 CEST 2007
> -----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
> ml#gal) in order to be able to analyse the nimblegen .tiff images in
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...
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