Hello All, Have there been any other efforts to accomodate ScanArray files in BASE since this last post in April?
Does anyone have any code to share that can convert the data in the Scanarray "Array Column, Array Row" fields to a single GPR-style "Array Block" field? Thanks, Jim Collett ******************************************** James R. Collett Ellington Laboratory Institute for Cellular and Molecular Biology MBB 3.424 2500 Speedway University of Texas Austin, TX 78712 Voice: 512.471.6087 Fax: 512.471.6097 ******************************************** From: Scott Givan <[EMAIL PROTECTED]> Re: scanarray CSV format & "array block" 2005-04-22 08:43 We"ve taken an approach related to your script idea. When someone uses the PE scanner, they upload their resulting data file using a web form that posts to a CGI script. The script takes the original data, calculates and adds the array block for each feature and uploads the new data file to BASE as user "generic". Every authenticated user has group read privileges for these files, so users can choose their reformatted files when associating raw data sets to scans. There"s a link on the BASE entry page to the web form, so people can find it easily. It"s an extra step, but it has worked reasonably well so far. scott The script generates the array block and for each feature and adds a column with this data. On Mar 25, 2005, at 12:49 PM, Danny Park wrote: > > Hi guys, > > We"re using a new scanner (and therefore new image analysis software) > extensively now called ScanArray from Perkin Elmer. It writes out > data in its own special CSV format. I can configure a result file > format in BASE to understand this file just fine, except for one thing > which I hadn"t realized was so important until now: the array block. > BASE expects the input data file to contain a single column indicating > which block/pin on the array each spot came from. Personally, I think > this is a reasonable expectation, all our GPR format files were like > this. Unfortunately ScanArray"s CSV files contain *two* columns: the > array block row and the array block column. > > Woe to me... all the information is there, and it"s so easy to write a > script to convert the two-column information into a single column, but > I really don"t want to introduce a step like that into the workflow of > our core facility (ie, "run this script on this file before you upload > it").. I"d rather modify the wizzzard code to somehow deal with it, > but it"s not so easy to figure out how to start. Currently the > wizzzard can accept the following types of values for fields it wants > in BASE: > > 1) a single column from the file, ex: \1\ > 2) a piece of text, ex: hello > 3) a string with multiple columns and other text, ex: "\1\ and \2\" > > I was thinking of giving it a fourth ability: > > 4) a simple mathematical expression, ex: \1\*4+\2\-4 > (which is exactly what I need.. for simplicity"s sake, we can say > no parentheses allowed) > > But maybe that"s a bit too complicated.. I was trying to figure out > how case 3 was achieved in the wizzzard code... it seems like if a > certain variable is an array, it goes for case 3.. so I"d have to > throw in some other variable or something. > > Options that won"t work for me: > > I. ScanArray"s "GPR format" option. It refuses to write more than > two channels of data in this format (I don"t understand why). The > whole reason for using this scanner was because we"re using 3 dyes > now. So that"s useless. > > II. Leave the array block blank. Write a transformation plug-in that > somehow interprets the position data and fills in the array block data > in the bioassayset. Not an option because in order to connect the > thing to an array design, it"s got to have the array block info from > the moment you upload it. > > III. Leave the array block blank and don"t use it. This is the way I > was going at first, but then I realized certain kinds of analysis we > wanted to do will require this field. > > -danny > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real > users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > The BASE general discussion mailing list > [EMAIL PROTECTED] > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Scott A. Givan Bioinformatics Coordinator Center for Gene Research and Biotechnology Oregon State University Corvallis, OR 97331-7303 [EMAIL PROTECTED] TEL: 541-737-9363 FAX: 541-737-3045 ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. 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