Hi I'm guessing the answer to my question is YES but are the Rb and Gb parts of read.maimages still compulsory ? Or can I some how ignore them ? I'm using some software (BlueFuse) that isn't supported by limma so I need to specify the column headers but the software doesn't give background values just values for Cy3 & Cy5 as it's approach is different to other spot finding programs. So at the moment I'm having to make new columns for the background and give them values of 0 for each gene. I've searched the mail achives and could only find this message from June 2003 I was asking just in case anything has changed since then OR is there an option for making Rb & Gb NULL or FALSE or something similar Cheers Jason Message: 4 Date: Thu, 19 Jun 2003 10:09:13 +1000 From: Gordon Smyth <smyth@wehi.edu.au> Subject: Re: [BioC] read.maimages The limma help documentation for 'read.maimages' says: columns: list with fields `Rf', `Gf', `Rb' and `Gb' giving the column names to be used for red and green foreground and background. So you need something like columns=list(Rf="Cy5",Gf="Cy3",Rb="Cy5.background",Gb="Cy3.backgrou nd") The names in double quotes are the column names in your file. The rest of the syntax is compulsory! -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

At 10:04 PM 3/02/2004, Jason Skelton wrote: >Hi >I'm guessing the answer to my question is YES but are the Rb and Gb parts >of read.maimages still compulsory ? >Or can I some how ignore them ? Short answer is yes. But you can work around this by reading arbitrary columns into Rb and Gb and then nulling them: RG <- read.maimages(files, souce=list(Rf="YourRedfg",Gf="YourGreenfg",Rb="YourRedfg","Gb="YourGre enfg") RG <- backgroundCorrect(RG, method="none") Gordon >I'm using some software (BlueFuse) that isn't supported by limma so I need >to specify the column headers but the software >doesn't give background values just values for Cy3 & Cy5 as it's approach >is different to other spot finding programs. >So at the moment I'm having to make new columns for the background and >give them values of 0 for each gene. > >I've searched the mail achives and could only find this message from June >2003 I was asking just in case anything has changed since then OR is there >an option for making Rb & Gb NULL >or FALSE or something similar > > >Cheers > >Jason > >Message: 4 >Date: Thu, 19 Jun 2003 10:09:13 +1000 >From: Gordon Smyth <smyth@wehi.edu.au> >Subject: Re: [BioC] read.maimages > > >The limma help documentation for 'read.maimages' says: > > columns: list with fields `Rf', `Gf', `Rb' and `Gb' giving the column > names to be used for red and green foreground and background. > >So you need something like > > columns=list(Rf="Cy5",Gf="Cy3",Rb="Cy5.background",Gb="Cy3.backgro und") > >The names in double quotes are the column names in your file. The rest of >the syntax is compulsory! > > > > >-- >-------------------------------- >Jason Skelton >Pathogen Microarrays >Wellcome Trust Sanger Institute >Hinxton >Cambridge >CB10 1SA > >Tel +44(0)1223 834244 Ext 7123 >Fax +44(0)1223 494919