Dear Eske, Well, the only BlueFuse output files that we have seen have the second line blank, hence the test for that. Are you saying that you have BlueFuse files with a different format? If so, it would help to see the header lines from one of your files. We have found it rather hard to get information about the BlueFuse format in order to support it. The BlueGnome people www.cambridgebluegnome.com) are friendly enough, but we haven't been able to get specific information from them. We have only seen two BlueFuse files, and can only base our limma support for the BlueFuse platform on what we've seen. We could supply robust support from BlueFuse files in limma if we had a clear definition of what the BlueFuse format is. It might help if BlueFuse clients such as yourself were to pursuade BlueGnome of the desirability of this. Best wishes Gordon > Date: Mon, 6 Mar 2006 10:46:55 +0100 > From: "Eskeatnaf, M.A." <eskeatnaf.ma at="" vumc.nl=""> > Subject: [BioC] bluefuse export and limma read.maimages > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <06Mar6.105633cet.336377 at nucleus.azvu.nl> > Content-Type: text/plain > > Dear all > I was trying to load a bluefuse file into R , by the read.maimages function but I am recieving the > error message > "Error in readBlueFuseHeader(fullname) : Second line not blank" > Could you please help me how to solve this > regards > eske > > > > ---------------------------------------------------------------- > VU medisch centrum. Kennis maakt ons beter. > Lustrum 20056 > www.5jaarvumc.nl

Hi All The second line in the bluefuse files I have access to are filled with hashes, rather than a blank line. Also there are 28 lines in the header instead of 16. I've found the easiest was to read them in using limma is to manually delete the hashes in the second row and remove the additional lines in the header i.e. lines 17- 28. Limma can then read the data in without issue. I hope that provides some help. Mike Smith On 7 Mar 2006 at 23:15, Gordon K Smyth wrote: > Dear Eske, > > Well, the only BlueFuse output files that we have seen have the second line blank, hence the test > for that. Are you saying that you have BlueFuse files with a different format? If so, it would > help to see the header lines from one of your files. > > We have found it rather hard to get information about the BlueFuse format in order to support it. > The BlueGnome people www.cambridgebluegnome.com) are friendly enough, but we haven't been able to > get specific information from them. We have only seen two BlueFuse files, and can only base our > limma support for the BlueFuse platform on what we've seen. > > We could supply robust support from BlueFuse files in limma if we had a clear definition of what > the BlueFuse format is. It might help if BlueFuse clients such as yourself were to pursuade > BlueGnome of the desirability of this. > > Best wishes > Gordon > > > > Date: Mon, 6 Mar 2006 10:46:55 +0100 > > From: "Eskeatnaf, M.A." <eskeatnaf.ma at="" vumc.nl=""> > > Subject: [BioC] bluefuse export and limma read.maimages > > To: <bioconductor at="" stat.math.ethz.ch=""> > > Message-ID: <06Mar6.105633cet.336377 at nucleus.azvu.nl> > > Content-Type: text/plain > > > > Dear all > > I was trying to load a bluefuse file into R , by the read.maimages function but I am recieving the > > error message > > "Error in readBlueFuseHeader(fullname) : Second line not blank" > > Could you please help me how to solve this > > regards > > eske > > > > > > > > ---------------------------------------------------------------- > > VU medisch centrum. Kennis maakt ons beter. > > Lustrum 20056 > > www.5jaarvumc.nl > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Dear Eske, It turns out that the format of BlueFuse files changed between versions 3.1 and 3.2 of that program. With info provided by Mike Smith, I've updated limma 2.4.11 to be able to read all versions of BlueFuse correctly. Best wishes Gordon > Date: Mon, 6 Mar 2006 10:46:55 +0100 > From: "Eskeatnaf, M.A." <eskeatnaf.ma at="" vumc.nl=""> > Subject: [BioC] bluefuse export and limma read.maimages > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <06Mar6.105633cet.336377 at nucleus.azvu.nl> > Content-Type: text/plain > > Dear all > I was trying to load a bluefuse file into R , by the read.maimages function but I am recieving the > error message > "Error in readBlueFuseHeader(fullname) : Second line not blank" > Could you please help me how to solve this > regards > eske > > > > ---------------------------------------------------------------- > VU medisch centrum. Kennis maakt ons beter. > Lustrum 20056 > www.5jaarvumc.nl