Re: [base] merged data
Julie Naito wrote: Is this the case with BASE version 1.2.16? Sorry, I assumed you were asking about BASE 2. I guess the statement about that the same sample must end up in the same channel is true also for BASE 1. I don't know if that requires different file formats or not in the Imagene case, but it does for Genepix. With Genepix the data headers are different so the dye swapped data can't be imported with the same file format and vice versa. I guess that if you try to import you will find out how to do it. /Nicklas Hello there. Do you need to create two separate result file formats for 2 separate Imagene merged raw data sets if 1 set includes a dye swap? Currently there is no plugin that can import Imagene data so the question is hypothetical (see http://base.thep.lu.se/ticket/450). If the plugin is implemented in a similar way as the existing raw data importer you will probably need two configurations. The important thing is that the same sample ends up in the same channel for both hybridizations. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] how can i interact with the spot creator plugin from outside the system
Greetings!
I'm trying to understand the genepix tiff spotfinding problem I described
earlier.
I want to interact with the spotfinder plugin with my own program but I
can't create files.
I have this:
images/
|-- 13298608_532-uncompressed.tif
`-- 13298608_635-uncompressed.tif
I want to do something like this:
public class TestImageProblem {
SpotImagesData data;
FileData red;
FileData green;
TestImageProblem() {
data = new SpotImagesData();
data.setGamma(new Float(1.8));
data.setXOffset(2000);
data.setYOffset(2400);
data.setXScale(10);
data.setYScale(10);
data.setSpotsize(24);
java.io.File redfile = new
java.io.File(images/13298608_635-uncompressed.tif);
java.io.File greenfile = new
java.io.File(images/13298608_532-uncompressed.tif);
Pass the data to the spot image creator ( SpotImages.createSpotImages )
}
Can you tell me how to create the appropriate file objects when the files
are here and not connected to the base datbaase?
Thanks!
Chad
-
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