BlueFuse in limmaGUI [was LimmaGUI Error]
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@gordon-smyth
Last seen 57 minutes ago
WEHI, Melbourne, Australia
>Date: Mon, 1 Aug 2005 15:29:51 -0500 >From: etbp2 at borcim.wustl.edu (Brooke-Powell, Elizabeth) >Subject: [BioC] LimmaGUI Error >To: <bioconductor at="" stat.math.ethz.ch=""> >Cc: Gordon K Smyth <smyth at="" wehi.edu.au=""> > >Hello there, > >I am writing for a second time to ask for some help with a LimmaGUI error I >am having. I am trying to load some BlueFuse results files into LimmaGUI. I >am able to load the data in (seen in R window as being read in). I am using >the other file type function in limmaGUI. This isn't a complete specification of what you did. What column names did you specify (for both foreground and background)? Since BlueFuse export files don't contain background intensities, have you tried setting the background correction method in limmaGUI to "none"? Gordon > I have no errors when reading the >information in, and I am also able to create an M box plot with no >normalization for all slides. The problem is that when I go to plot an M box >plot with any combination of normalization (either within norm and/or >between slide normalization) I get the following errors: > >Error: subscript out of bounds > >Then > >Error in assign ("MAwithinArrays", MA, limmaGUIenvironment) : Object "MA" >not found. > >I am using R in Windows XP, version R 2.1.1 and LimmaGUI version 1.3.9 > >Please help.... > >Liz
Normalization GO limmaGUI ASSIGN Normalization GO limmaGUI ASSIGN • 590 views
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@brooke-powell-elizabeth-1185
Last seen 7.2 years ago
Thank you all for you responses. I am sorry I didn't give enough information. I have done what I have always done with BlueFuse, I have told LimmaGUI not to use background correction or spot quality calls as it cannot with non GenePix, Spot etc files. When using the other file type function I set the foreground and background to be the same header (so the Cy5 foreground and background are AMPCH2 and cy3 is AMPCH1). If I don't use a header it recognizes it won't load. This has never been a problem in the past as I tell it to ignore background. The problem doesn't seem to be in the file loading, but rather in the M box plot generation with normalization. LimmaGUI is taking in all the data, targets file and spot types, and can generate a an M box plot without normalization. I loaded some ScanArray files in the same way and that worked just fine including the normalization. I am beginning to believe that the problem is when I use BlueFuse Fused data out put files... I am just not sure why.... Hope that adds some more information... Liz -----Original Message----- From: Gordon Smyth [mailto:smyth@wehi.edu.au] Sent: Tuesday, August 02, 2005 5:27 AM To: Brooke-Powell, Elizabeth Cc: bioconductor at stat.math.ethz.ch Subject: [BioC] BlueFuse in limmaGUI [was LimmaGUI Error] >Date: Mon, 1 Aug 2005 15:29:51 -0500 >From: etbp2 at borcim.wustl.edu (Brooke-Powell, Elizabeth) >Subject: [BioC] LimmaGUI Error >To: <bioconductor at="" stat.math.ethz.ch=""> >Cc: Gordon K Smyth <smyth at="" wehi.edu.au=""> > >Hello there, > >I am writing for a second time to ask for some help with a LimmaGUI error I >am having. I am trying to load some BlueFuse results files into LimmaGUI. I >am able to load the data in (seen in R window as being read in). I am using >the other file type function in limmaGUI. This isn't a complete specification of what you did. What column names did you specify (for both foreground and background)? Since BlueFuse export files don't contain background intensities, have you tried setting the background correction method in limmaGUI to "none"? Gordon > I have no errors when reading the >information in, and I am also able to create an M box plot with no >normalization for all slides. The problem is that when I go to plot an M box >plot with any combination of normalization (either within norm and/or >between slide normalization) I get the following errors: > >Error: subscript out of bounds > >Then > >Error in assign ("MAwithinArrays", MA, limmaGUIenvironment) : Object "MA" >not found. > >I am using R in Windows XP, version R 2.1.1 and LimmaGUI version 1.3.9 > >Please help.... > >Liz
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At 01:41 AM 3/08/2005, Brooke-Powell, Elizabeth wrote: >Thank you all for you responses. I am sorry I didn't give enough >information. > >I have done what I have always done with BlueFuse, I have told LimmaGUI not >to use background correction or spot quality calls How exactly have you told it not to background correct? The exact sequence of reading in and dialog boxes. > as it cannot with non >GenePix, Spot etc files. Yes it can, with any program that gives background estimates, i.e., anything other than BlueFuse. > When using the other file type function I set the >foreground and background to be the same header (so the Cy5 foreground and >background are AMPCH2 and cy3 is AMPCH1). If I don't use a header it >recognizes it won't load. This has never been a problem in the past as I >tell it to ignore background. Are you saying that the analysis that you are doing works in a previous version of limmaGUI, but not in the version you are using? Gordon > The problem doesn't seem to be in the file >loading, but rather in the M box plot generation with normalization. >LimmaGUI is taking in all the data, targets file and spot types, and can >generate a an M box plot without normalization. I loaded some ScanArray >files in the same way and that worked just fine including the normalization. >I am beginning to believe that the problem is when I use BlueFuse Fused data >out put files... I am just not sure why.... > >Hope that adds some more information... > >Liz > >-----Original Message----- >From: Gordon Smyth [mailto:smyth at wehi.edu.au] >Sent: Tuesday, August 02, 2005 5:27 AM >To: Brooke-Powell, Elizabeth >Cc: bioconductor at stat.math.ethz.ch >Subject: [BioC] BlueFuse in limmaGUI [was LimmaGUI Error] > > > >Date: Mon, 1 Aug 2005 15:29:51 -0500 > >From: etbp2 at borcim.wustl.edu (Brooke-Powell, Elizabeth) > >Subject: [BioC] LimmaGUI Error > >To: <bioconductor at="" stat.math.ethz.ch=""> > >Cc: Gordon K Smyth <smyth at="" wehi.edu.au=""> > > > >Hello there, > > > >I am writing for a second time to ask for some help with a LimmaGUI error I > >am having. I am trying to load some BlueFuse results files into LimmaGUI. I > >am able to load the data in (seen in R window as being read in). I am using > >the other file type function in limmaGUI. > >This isn't a complete specification of what you did. What column names did >you specify (for both foreground and background)? > >Since BlueFuse export files don't contain background intensities, have you >tried setting the background correction method in limmaGUI to "none"? > >Gordon > > > I have no errors when reading the > >information in, and I am also able to create an M box plot with no > >normalization for all slides. The problem is that when I go to plot an M >box > >plot with any combination of normalization (either within norm and/or > >between slide normalization) I get the following errors: > > > >Error: subscript out of bounds > > > >Then > > > >Error in assign ("MAwithinArrays", MA, limmaGUIenvironment) : Object "MA" > >not found. > > > >I am using R in Windows XP, version R 2.1.1 and LimmaGUI version 1.3.9 > > > >Please help.... > > > >Liz
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Hi Gordon, Thank you for your help, I am saying that in previous versions of LimmaGUI I have not had a problem loading and analyzing BlueFuse data. I load the data in following LimmaGUI's series of pop up boxes. First it brings up as box asking where the files are, I tell it where the gal file is and then the targets file and finally the spot types... it then asks what type of results files I have, I click on the other box (because there is no BlueFuse option), and then get the box asking what the column headers are for the foreground and background for each of the channels. I type in AMPCH2 for the Cy5 (foreground and background), then I type in AMPCH1 for Cy3 (fore and background) then it goes onto to the pop up box asking if I want to use background correction, I select no, and then a pop up window appears for spot weighting and If I select yes it tells me that I can only use it when I load the data in using the preset formats (in the window where I select other) for GenePix and yes all other file types except BlueFuse. If I continue it then tells me it will continue without spot weighting... so I always select no spot weighting as why see the error... One on the side problem is that if for example I want to use GenePix data, but not read in the mean data column (that last I knew was preset data column for GenePix files), but rather the median data; I need to use the other function in the results file type so I tell LimmaGUI which columns to look at and then select yes in the spot weighting window it still will not allow me to then say which column has flag data so it cannot use spot weight for GenePix data in this instance...... I have been using LimmaGUI since it came out and over the last few years have had no major problems. Through loading many types of data files and comparing them to the ScanArray files I also have I have narrowed down to what is causing the error. The problem is not in using BlueFuse data files, but rather Fused BlueFuse data files... The fusion combines on slide replicates and out puts a different results file (looks the same just only has one data point per oligo control etc). I am thinking the problem is coming form the fact that the gal file has replicates separated and the results files doesn't. I am not sure why this matters for plotting an M box plot, but do realize it might be a problem later on in analysis (although I cannot use the replicate spot function as our replicates are in the same blocks so I always keep the reps separate). Hope that adds further clarification, Liz -----Original Message----- From: Gordon Smyth [mailto:smyth@wehi.edu.au] Sent: Tuesday, August 02, 2005 6:24 PM To: Brooke-Powell, Elizabeth Cc: bioconductor at stat.math.ethz.ch Subject: RE: BlueFuse in limmaGUI [was LimmaGUI Error] At 01:41 AM 3/08/2005, Brooke-Powell, Elizabeth wrote: >Thank you all for you responses. I am sorry I didn't give enough >information. > >I have done what I have always done with BlueFuse, I have told LimmaGUI not >to use background correction or spot quality calls How exactly have you told it not to background correct? The exact sequence of reading in and dialog boxes. > as it cannot with non >GenePix, Spot etc files. Yes it can, with any program that gives background estimates, i.e., anything other than BlueFuse. > When using the other file type function I set the >foreground and background to be the same header (so the Cy5 foreground and >background are AMPCH2 and cy3 is AMPCH1). If I don't use a header it >recognizes it won't load. This has never been a problem in the past as I >tell it to ignore background. Are you saying that the analysis that you are doing works in a previous version of limmaGUI, but not in the version you are using? Gordon
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At 03:19 AM 4/08/2005, Brooke-Powell, Elizabeth wrote: >Hi Gordon, > >Thank you for your help, I am saying that in previous versions of LimmaGUI I >have not had a problem loading and analyzing BlueFuse data. I load the data >in following LimmaGUI's series of pop up boxes. First it brings up as box >asking where the files are, I tell it where the gal file is and then the >targets file and finally the spot types... it then asks what type of results >files I have, I click on the other box (because there is no BlueFuse >option), and then get the box asking what the column headers are for the >foreground and background for each of the channels. I type in AMPCH2 for the >Cy5 (foreground and background), then I type in AMPCH1 for Cy3 (fore and >background) then it goes onto to the pop up box asking if I want to use >background correction, I select no, and then a pop up window appears for >spot weighting and If I select yes it tells me that I can only use it when I >load the data in using the preset formats (in the window where I select >other) for GenePix and yes all other file types except BlueFuse. If I >continue it then tells me it will continue without spot weighting... so I >always select no spot weighting as why see the error... One on the side >problem is that if for example I want to use GenePix data, but not read in >the mean data column (that last I knew was preset data column for GenePix >files), but rather the median data; I need to use the other function in the >results file type so I tell LimmaGUI which columns to look at and then >select yes in the spot weighting window it still will not allow me to then >say which column has flag data so it cannot use spot weight for GenePix data >in this instance...... > >I have been using LimmaGUI since it came out and over the last few years >have had no major problems. Through loading many types of data files and >comparing them to the ScanArray files I also have I have narrowed down to >what is causing the error. The problem is not in using BlueFuse data files, >but rather Fused BlueFuse data files... The fusion combines on slide >replicates and out puts a different results file (looks the same just only >has one data point per oligo control etc). I am thinking the problem is >coming form the fact that the gal file has replicates separated and the >results files doesn't. Yes, this is almost certainly the problem. It sounds like you have a gene list which is a different length to your expression matrices, and that's a fatal problem. One way for you to go would be to stick to the non-fused data files. I am meeting with programmers to try to address this problem, in the sense that it is not necessary to have a separate GAL file with BlueFuse data. I am seeking to "retire" the use of GAL files except with SPOT data. This may enable you to work with fused files. Gordon > I am not sure why this matters for plotting an M box >plot, but do realize it might be a problem later on in analysis (although I >cannot use the replicate spot function as our replicates are in the same >blocks so I always keep the reps separate). > >Hope that adds further clarification, > >Liz
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