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Question: Single channel array, limma and imagene
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gravatar for Carla Zammit
6.9 years ago by
Carla Zammit40
Carla Zammit40 wrote:
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_Agil ent_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/carlazammi t/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/Deskto p/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 > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > 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 > _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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