
Just for others that might have the same problem: the files were in the correct format (.txt) but I had to change them over from a MS-DOS Formatted Text (.txt) to Windows Formatted Text (.txt) or a Tab Delimited Text (.txt) to import them into R successfully.

From: czammit@hotmail.com
To: jmacdon@med.umich.edu
Date: Wed, 8 Dec 2010 14:03:51 +0800
CC: bioconductor@r-project.org
Subject: Re: [BioC] Single channel array, limma and imagene

 
 
 
Hi Jim,
 
 
 
I have tried a couple of things to try to get
this to work. Just as a side note I am on a mac v.10.4.11 so am running biocinstall version 2.2.11 with R version 2.7.0.
 
 
 
As I am using Imagene data files the program,
as you know, looks for the Cy3 and corresponding Cy5 files. So my first
attempts were aimed at trying to make a "false" Cy5 files, with or
without the conditions was also preformed.
 
 
 
 
 
  
  SlideNumber
  
  
  FileNameCy3
  
  
  FileNameCy5
  
  
  Cy3
  
  
  Cy5
  
 
 
  
  3
  
  
  3E.txt
  
  
  11G.txt
  
  
  1
  
  
  0
  
 
 
  
  4
  
  
  4F.txt
  
  
  12H.txt
  
  
  0
  
  
  1
  
 
 
  
  5
  
  
  5E.txt
  
  
  13G.txt
  
  
  1
  
  
  0
  
 
 
  
  6
  
  
  6F.txt
  
  
  14H.txt
  
  
  0
  
  
  1
  
 
 
  
  7
  
  
  7E.txt
  
  
  15G.txt
  
  
  1
  
  
  0
  
 
 
  
  8
  
  
  8F.txt
  
  
  16H.txt
  
  
  0
  
  
  1
  
 
 
 
 
 
> targets <- readTargets()
 
> files <-
targets[,c("FileNameCy3","FileNameCy5")]
 
> RG <- read.maimages(files,
source="imagene")
 
 
 
The following error resulted:
 
Read header information
 
Error in read.imagene(files = files, path =
path, ext = ext, names = names,  : 
 
 
Can't find Field Dimensions in ImaGene header
 
In addition: Warning messages:
 
1: In readLines(con, n = 1) : incomplete final
line found on '3E.txt'
 
2: In readImaGeneHeader(fullname) :
 
 
End of file encountered before End Header
 
 
 
This is a problem with all the files not solely 3E.txt And the second method I tried to use was based
on this method
(http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma),
as follows:
 
 
 
 
 
  
  SlideNumber
  
  
  FileName
  
  
  Condition
  
 
 
  
  1
  
  
  3E.txt
  
  
  1
  
 
 
  
  2
  
  
  4F.txt
  
  
  0
  
 
 
  
  3
  
  
  5E.txt
  
  
  1
  
 
 
  
  4
  
  
  6F.txt
  
  
  0
  
 
 
  
  5
  
  
  7E.txt
  
  
  1
  
 
 
  
  6
  
  
  8F.txt
  
  
  0
  
 
 
 
 
 
> targets <- readTargets()
 
> RG <-
read.maimages(targets,path="/Users/carlazammit/Desktop/Gold/Data to
analyze/Microarray CH34 Carla 2010/Raw Data", columns = list(G =
"gMedianSignal", Gb = "gBGMedianSignal", R =
"gProcessedSignal", Rb = "gIsPosAndSignif"), annotation =
c("Row", "Col","FeatureNum",
"ControlType","ProbeName"))
 
or 
 
> RG <- read.maimages(targets,source="generic",path="/Users/carlazammit/Desktop/Gold/Data
to analyze/Microarray CH34 Carla 2010/Raw Data", columns = list(G =
"gMedianSignal", Gb = "gBGMedianSignal", R =
"gProcessedSignal", Rb = "gIsPosAndSignif"), annotation =
c("Row", "Col","FeatureNum",
"ControlType","ProbeName"))
 
 
 
This managed to read the files but an error was
created:
 
 
 
Error in readGenericHeader(fullname, columns =
columns) : Specified column headings not found in file
 
In addition: There were 50 or more warnings (use
warnings() to see the first 50)
 
> warnings()
 
Warning messages:
 
1...50: In grep(a, txt) ... : input string 1 is
invalid in this locale
 
 
 
I also attempted
 
> RG <-
read.maimages(targets,source="imagene",path="/Users/carlazammit/Desktop/Gold/Data
to analyze/Microarray CH34 Carla 2010/Raw Data", columns = list(G =
"gMedianSignal", Gb = "gBGMedianSignal", R =
"gProcessedSignal", Rb = "gIsPosAndSignif"), annotation =
c("Row", "Col","FeatureNum",
"ControlType","ProbeName"))
 
and
 
 
 
Which came up with the error
 
Error in read.imagene(files = files, path = path, ext =
ext, names = names, : Need a two column matrix of file names
 
 
 
But when I loaded the two column matrix I was
faced with the same error as above.
 
 
 
The headings are all matched properly from the
3E-8F.txt files and I have not manipulated these files at all and they are all the same length so am completely
unsure of the problem. I have attached the first couple of rows of my array
file 3E to see if there is a problem there. 
 
 
 
Any help would be greatly appreciated, thank you.
 
 
 
Regards
 
Carla
 
 
 
 
 
> Date: Tue, 7 Dec 2010 09:37:43 -0500
> From: jmacdon@med.umich.edu
> To: czammit@hotmail.com
> CC: bioconductor@r-project.org
> Subject: Re: [BioC] Single channel array, limma and imagene
> 
> Hi Carla,
> 
> On 12/6/2010 8:15 PM, Carla Zammit wrote:
> >
> >
> > Hi All,
> > I am new to microarray analysis but have spent some time trying to solve/research my problem but as yet have not prevailed.
> > I have inherited some single-channel microarray data produced using Imagene, I have tried to find a good workflow to do annalyze the data but have been unable to find something that works for the Imagene data files.
> > Has anybody dealt with single-channel Imagene data using Limma before, if so can you point me in the right direction? (I have searched through the archives, have the Limma manual and a couple of the recommended text) If there is no guide available I will post my script and hopefully someone can help.
> > Thank you.
> 
> I think you will need to give more information than that. Imagene is one 
> of the platforms that are directly targeted by this package (see e.g., 
> ?read.imagene), and there are arguments to that function specifically 
> for single-channel data.
> 
> In addition, starting on p. 31 of the limma User's Guide, there is 
> information about handling single-channel data.
> 
> If you can give specific things that are confusing to you, perhaps 
> someone can help.
> 
> Best,
> 
> Jim
> 
> 
> > Regards,Carla
> >
> >   		 	   		
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> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
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