If you are using the BASE 1 implementation of lowess the source is available in directory base-1.2.17/plugins/src/normalizers/. You can douwnload the latest BASE 1.2.17b source from http://base1.thep.lu.se/ (select 'Download BASE' in the left margin).
You cannot directly run the BASE 2 implementation of the lowess plug-in outside the BASE 2 application. Doing this requires changes to the code, and the header you present will not be valid. If you want to use lowess as a stand alone tool you should go for the BASE 1.2 implementation. Cheers, Jari George Wu wrote: > > 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]
