Thanks, Jari. The problem happened with Base 1 version. We set up your lowess as standalone version so that we can run command like: cat input.txt | lowess > output.txt on Solaris unix.
In input file, we used header like the following. Can we use the same header format to run your BASE2 Java version? If not, could you provide a header sample? Thanks, George BASEfile section lowess settings fit_fraction 0.33 min_x_step 0.1 n_iter 4 % section assays count 2 columns id name annotationColumns % 1 temp section spots columns position reporter assayData assayFields intensity1 intensity2 assays 1 % 0 1 1276 1491 1 1 2096 790 2 1 1146 5017 -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jari Häkkinen Sent: Thursday, May 03, 2007 8:35 AM To: BASE ML Subject: Re: [base] Base Lowess normalization program Hi, I assume you are referring to the BASE 2 implementation of lowess. The lowess plug-in is a part of the BASE core and is available in source form in the source package downloadable from the base web site. You can browse the code at http://base.thep.lu.se/browser/trunk/src/plugins/core/net/sf/basedb/plugins/ LowessNormalization.java We have no reported issues with the plug-in but we have not tested 244k arrays. It may be out of memory issues, can you check the logs for messages related to the problem. Jari George Wu wrote: > Dear All: > > I am using Base Lowess program to normalize my Microarray data. But seems it > works with my small dataset input (e.g. 44k-probe records). But it doesn't > work with my big data input file (e.g. 244K-probe array). > > So does Lowess have data file size limitation? If so, how can I fix it? By > the way, I only have the executable? Is there any way I could get source > code? > > Thank you very much, > > George > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
