[BioC] Single channel array, limma and imagene

Wed Dec 8 07:03:51 CET 2010

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 at med.umich.edu
> To: czammit at hotmail.com
> CC: bioconductor at 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
> >
> >   		 	   		
> > 	[[alternative HTML version deleted]]
> >
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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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