limmaGUI: target file and spot file
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@jamila-bernardi-2943
Last seen 7.2 years ago
Dear all, I'm working with the interface limmaGUI using data from two-colors spotted arrays generated by GenePix scanner. I have two basic problems regarding the input data: 1) after giving gal file and target file and after background correction the software doesn't proceed to analysis and it sends this message "limmaGUI was unable to read the image processing files listed in the targets file". I have this problem with recent data, but with previous data the package worked. Why?I have changed nothing in the procedure (analysis of images and exporting txt file). 2) the package doesn't read my spot file, I ask some help to prepare correctly this type of input file. Thanks to everybody. Jam Posta, news, sport, oroscopo: tutto in una sola pagina. Crea l'home page che piace a te! www.yahoo.it/latuapagina [[alternative HTML version deleted]]
limmaGUI limmaGUI • 727 views
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Mark Cowley ▴ 910
@mark-cowley-2951
Last seen 7.2 years ago
Hi Jamila, I noticed that you have not yet received a response. Generally, if limmaGUI is having a hard time importing your files, then limma itself will also have a hard time. I'd recommend that you read the limma users guide (type limmaUserGuide() to bring this pdf up) and get to a point where you can at least import your data using the non-GUI version. If you then still don't feel comfortable using limma itself, then you should be able to proceed again using limmaGUI, but this time with the correct targets (and spot types) file. If you still need help, then please post back to the list with more information, particularly the spot types file that you are currently using mark ----------------------------------------------------- Mark Cowley, BSc (Bioinformatics)(Hons) Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- On 25/07/2008, at 8:08 PM, Jamila Bernardi wrote: > > > Dear all, > I'm working with the interface limmaGUI using data from two-colors > spotted arrays generated by GenePix scanner. > I have two basic problems regarding the input data: > 1) after giving gal file and target file and after background > correction the software doesn't proceed to analysis and it sends > this message "limmaGUI was unable to read the image processing files > listed in the targets file". I have this problem with recent data, > but with previous data the package worked. Why?I have changed > nothing in the procedure (analysis of images and exporting txt file). > 2) the package doesn't read my spot file, I ask some help to prepare > correctly this type of input file. > Thanks to everybody. > Jam > > > Posta, news, sport, oroscopo: tutto in una sola pagina. > Crea l'home page che piace a te! > www.yahoo.it/latuapagina > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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I used limmaGUI in teh past, and whenever I had problems similar to the one described here I could trace the problem back to either wrongly typed file names in the Targets file (or in the wrong folder) or wrong column names in teh files (at least wrong in teh sense that teh defaults didn't correspond to what I had on my files). You only need one file to be problematic to get the error. So I'd say you shoudl recheck that the names are all good (a space after a file name can be a problem, so make sure you check well) and then that the column names in all teh files are what's expected. I'd agree with Mark... try to use limma to read your files. It may seem difficult at first, compared to limmaGUI, but it really isn't when you look at it (check the user's guide) and it's a lot faster when you're testing whether your files are correct etc. Jose Quoting Mark Cowley <m.cowley at="" garvan.org.au="">: > Hi Jamila, > I noticed that you have not yet received a response. > Generally, if limmaGUI is having a hard time importing your files, then > limma itself will also have a hard time. I'd recommend that you read > the limma users guide (type limmaUserGuide() to bring this pdf up) and > get to a point where you can at least import your data using the > non-GUI version. > If you then still don't feel comfortable using limma itself, then you > should be able to proceed again using limmaGUI, but this time with the > correct targets (and spot types) file. > > If you still need help, then please post back to the list with more > information, particularly the spot types file that you are currently > using > > mark > ----------------------------------------------------- > Mark Cowley, BSc (Bioinformatics)(Hons) > > Peter Wills Bioinformatics Centre > Garvan Institute of Medical Research, Sydney, Australia > ----------------------------------------------------- > > On 25/07/2008, at 8:08 PM, Jamila Bernardi wrote: > >> >> >> Dear all, >> I'm working with the interface limmaGUI using data from two-colors >> spotted arrays generated by GenePix scanner. >> I have two basic problems regarding the input data: >> 1) after giving gal file and target file and after background >> correction the software doesn't proceed to analysis and it sends >> this message "limmaGUI was unable to read the image processing >> files listed in the targets file". I have this problem with recent >> data, but with previous data the package worked. Why?I have changed >> nothing in the procedure (analysis of images and exporting txt >> file). >> 2) the package doesn't read my spot file, I ask some help to >> prepare correctly this type of input file. >> Thanks to everybody. >> Jam >> >> >> Posta, news, sport, oroscopo: tutto in una sola pagina. >> Crea l'home page che piace a te! >> www.yahoo.it/latuapagina >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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