Doh! As I suspected... it turns out that the problem was at my end.
There was one problematic (unexpectedly duplicated) hybridization in the experiment I'm uploading and it just so happened to be the first one I tried to create spot images for... The raw data and tiff image did not correspond to each other - no surprise that the spots didn't line up! sorry to those who wasted energy reading my mail and this one! cheers, Bob. Bob MacCallum writes: > > Hi, > > Has anyone had trouble creating the jpeg spot images from GenePix files? All > the software works without complaining, but the spots all seem to be in the > wrong place: not centred and they don't seem to correspond to the raw data. > I've only tried this one file and I'm guessing that the problem lies at our > end, but any help or advice would be appreciated (it seems there's nothing in > the mailing list archive about this). > > > Here's some of the (I hope) relevant info > > >From the .gpr file: > > "Type=GenePix Results 1.4" > "Scanner=GenePix 4000B [83298]" > "PixelSize=10" > "ImageOrigin=2000, 5120" > "JpegOrigin=2000, 5220" > "Creator=GenePix Pro 3.0.6.53" > > And the auto-detected settings for spot extraction: > > Spot image size: 16 > Scale for coordinates: 10 > Image X offset: 2000 > Image Y offset: 5120 > Index of red TIFF: 3 (but this has to be changed to 1) > Index of green TIFF: 4 (but this has to be changed to 2) > > The first few rows of X and Y columns data from the .gpr file: > > 2190 5540 > 2400 5530 > 2610 5540 > 2820 5540 > (and I checked that the same values are in BASE) > > I also tried offsets of (0,0) but that caused an out-of-bounds > error in the spot extractor. > > > thanks for any advice you might have, > > cheers, > Bob. > > -- > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > Division of Cell and Molecular Biology | Imperial College London | > Phone +442075941945 | Email [EMAIL PROTECTED] > > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
