[BioC] Single channel array, limma and imagene
James W. MacDonald
jmacdon at med.umich.edu
Wed Dec 8 15:52:44 CET 2010
Hi Carla,
On 12/8/2010 1:03 AM, Carla Zammit wrote:
>
>
>
> 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.
I'm not sure why you are still running R 2.7.0, as the OS isn't really
relevant. You should upgrade to 2.12.0 (right now!), as two-year old
software in the Open Source community is neither supported nor really
even remembered.
You should also note that contrary to claims by Apple, you can directly
upgrade to Snow Leopard from Tiger (as Google will attest). Given that
the Snow Leopard disk costs something like $35, there is really no
reason to be running Tiger.
>
>
>
> 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.
That is unnecessary. See ?read.imagene, specifically
green.only: logical, for use with 'source', should the green (Cy3)
channel only be read, or are both red and green required?
The columns argument may also be relevant:
columns: list, or named character vector. For two color data, this
should have fields 'R', 'G', 'Rb' and 'Gb' giving the column
names to be used for red and green foreground and background
or, in the case of Imagene data, a list with fields 'f' and
'b'. For single channel data, the fields are usually 'E' and
'Eb'. This argument is optional if 'source' is specified,
otherwise it is required.
Best,
Jim
>
>
>
>
>
>
> 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.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
>>
>
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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