Hello, I am using limma package to read my data into R, and I use the following command to read gal file to get layout, however, I got the following error messages, > RG$genes<-readGAL(galfile="GID.gal",path="") Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 4411 did not have 5 elements and I did check line 4411, there ARE 5 elements. I do not know why this error occur. Any suggestion are greatly appreciated ******************************** Joyce Gu M.S. Scientific Programmer Cancer Genomics Group Baylor College of Medicine Phone: 832-824-4680 Fax: 832-825-4038

Hi All, What are the different ways of detecting bad cDNA or oligo arrays using bioconductor packages? Also, what are some of the quality measures of replicates arrays (other than standard deviations)? Basically, we are always looking at many arrays (>20) simultaneously. I want to be able to screen thru arrays and pick out the bad arrays quickly. Any ideas? Thanks in advance! Anna

Hi Joyce, If line 4411 has the appropriate number of elements, check that they are tab separated in the same way as the preceding lines. If they are, then I'm not sure what the problem is. Perhaps you can send the gal file or line 4411 and a few of the lines before it so I can take a look? Best wishes, Matt Ritchie > Hello, > I am using limma package to read my data into R, and I use the following > command to read gal file to get layout, however, I got the following > error messages, >> RG$genes<-readGAL(galfile="GID.gal",path="") > Error in scan(file = file, what = what, sep = sep, quote = quote, dec = > dec, : > line 4411 did not have 5 elements > > and I did check line 4411, there ARE 5 elements. I do not know why this > error occur. > Any suggestion are greatly appreciated > > ******************************** > Joyce Gu M.S. > Scientific Programmer > > Cancer Genomics Group > Baylor College of Medicine > Phone: 832-824-4680 > Fax: 832-825-4038

Hi Matthew, I got this work now. Thank you very much! Joyce >===== Original Message From "Matthew Ritchie" <mritchie@wehi.edu.au> ===== >Hi Joyce, > >If line 4411 has the appropriate number of elements, check that they are >tab separated in the same way as the preceding lines. If they are, then >I'm not sure what the problem is. Perhaps you can send the gal file or >line 4411 and a few of the lines before it so I can take a look? Best >wishes, > >Matt Ritchie > >> Hello, >> I am using limma package to read my data into R, and I use the following >> command to read gal file to get layout, however, I got the following >> error messages, >>> RG$genes<-readGAL(galfile="GID.gal",path="") >> Error in scan(file = file, what = what, sep = sep, quote = quote, dec = >> dec, : >> line 4411 did not have 5 elements >> >> and I did check line 4411, there ARE 5 elements. I do not know why this >> error occur. >> Any suggestion are greatly appreciated >> >> ******************************** >> Joyce Gu M.S. >> Scientific Programmer >> >> Cancer Genomics Group >> Baylor College of Medicine >> Phone: 832-824-4680 >> Fax: 832-825-4038