read.maimages in limma package
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@giusy-della-gatta-3197
Last seen 8.1 years ago
Hi! I am analyzing custom two color agilent array by using limma package and I am having some problems with the read.maimages comand: I launch this comand: > read.maimages("Targets$Filename, source="agilent") and the error that I have is the following: Read Control_2b.txt Read Control_3b.txt Error in readGenericHeader(fullname, columns = columns) : Specified column headings not found in file It is like the columns in the file that I gave as input (Control_.txt) are not recognized, maybe I have this problem because is a custom agilent array? If this is the problem, I have to specify in my script the following informations: 1. list with fields R, G, Rb and Gb giving the column names to be used for red and green foreground and background; 2. character vector of names of other columns to be read containing spot-specific information; 3. character vector of names of columns containing annotation information about the probes; Is there someone that can answer me and that has got some experience in the two color agilent custom array analysis? Thank you in advance Giusy
limma limma • 1.9k views
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@giusy-della-gatta-3197
Last seen 8.1 years ago
Thank you Peter, I'll check it out! I have also seen that I have to make a file in which I have to describe agilent annotations (see point 3 of my previuos email). May you know where I have to check to retrieve informations on the file format that I have to use? Thank you G -----Original Message----- From: john seers (IFR) [mailto:john.seers@bbsrc.ac.uk] Sent: Wed 12/17/2008 4:36 AM To: Giusy Della Gatta; bioconductor at stat.math.ethz.ch Subject: RE: [BioC] read.maimages in limma package Hi Giusy If you look at the code for read.maimages you can see which columns limma is expecting for agilent: agilent = list(G = "gMeanSignal", Gb = "gBGMedianSignal", R = "rMeanSignal", Rb = "rBGMedianSignal"), If your custom arrays do not match these names then you have to specify them yourself (using the columns parameter of read.maimages). Regards John Seers --- Hi! I am analyzing custom two color agilent array by using limma package and I am having some problems with the read.maimages comand: I launch this comand: > read.maimages("Targets$Filename, source="agilent") and the error that I have is the following: Read Control_2b.txt Read Control_3b.txt Error in readGenericHeader(fullname, columns = columns) : Specified column headings not found in file It is like the columns in the file that I gave as input (Control_.txt) are not recognized, maybe I have this problem because is a custom agilent array? If this is the problem, I have to specify in my script the following informations: 1. list with fields R, G, Rb and Gb giving the column names to be used for red and green foreground and background; 2. character vector of names of other columns to be read containing spot-specific information; 3. character vector of names of columns containing annotation information about the probes; Is there someone that can answer me and that has got some experience in the two color agilent custom array analysis? Thank you in advance Giusy _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Giusy >1. list with fields R, G, Rb and Gb giving the column names to be used >for red and green foreground and background; As already discussed. >2. character vector of names of other columns to be read containing >spot-specific information; Use other.names= parameter of read.maimages. I have not used this so I cannot say any more. >3. character vector of names of columns containing annotation >information about the probes; Use the annotation= parameter of read.maimages to set the annotation columns. No file involved unless I have misunderstood you. Looking at your previous email more closely I am a bit puzzled as it looks like you may have read one array (Read Control_2b.txt) in successfully. If so it must have standard Agilent column names. Perhaps your second array file has a problem? >Read Control_2b.txt >Read Control_3b.txt >Error in readGenericHeader(fullname, columns = columns) : >Specified column headings not found in file Regards John (or is it Peter) Seers --- -----Original Message----- From: Giusy Della Gatta [mailto:Gatta@icg.cpmc.columbia.edu] Sent: 17 December 2008 13:25 To: john seers (IFR); bioconductor at stat.math.ethz.ch Subject: RE: [BioC] read.maimages in limma package Thank you Peter, I'll check it out! I have also seen that I have to make a file in which I have to describe agilent annotations (see point 3 of my previuos email). May you know where I have to check to retrieve informations on the file format that I have to use? Thank you G -----Original Message----- From: john seers (IFR) [mailto:john.seers@bbsrc.ac.uk] Sent: Wed 12/17/2008 4:36 AM To: Giusy Della Gatta; bioconductor at stat.math.ethz.ch Subject: RE: [BioC] read.maimages in limma package Hi Giusy If you look at the code for read.maimages you can see which columns limma is expecting for agilent: agilent = list(G = "gMeanSignal", Gb = "gBGMedianSignal", R = "rMeanSignal", Rb = "rBGMedianSignal"), If your custom arrays do not match these names then you have to specify them yourself (using the columns parameter of read.maimages). Regards John Seers --- Hi! I am analyzing custom two color agilent array by using limma package and I am having some problems with the read.maimages comand: I launch this comand: > read.maimages("Targets$Filename, source="agilent") and the error that I have is the following: Read Control_2b.txt Read Control_3b.txt Error in readGenericHeader(fullname, columns = columns) : Specified column headings not found in file It is like the columns in the file that I gave as input (Control_.txt) are not recognized, maybe I have this problem because is a custom agilent array? If this is the problem, I have to specify in my script the following informations: 1. list with fields R, G, Rb and Gb giving the column names to be used for red and green foreground and background; 2. character vector of names of other columns to be read containing spot-specific information; 3. character vector of names of columns containing annotation information about the probes; Is there someone that can answer me and that has got some experience in the two color agilent custom array analysis? Thank you in advance Giusy _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@john-seers-ifr-1605
Last seen 8.1 years ago
Hi Giusy If you look at the code for read.maimages you can see which columns limma is expecting for agilent: agilent = list(G = "gMeanSignal", Gb = "gBGMedianSignal", R = "rMeanSignal", Rb = "rBGMedianSignal"), If your custom arrays do not match these names then you have to specify them yourself (using the columns parameter of read.maimages). Regards John Seers --- Hi! I am analyzing custom two color agilent array by using limma package and I am having some problems with the read.maimages comand: I launch this comand: > read.maimages("Targets$Filename, source="agilent") and the error that I have is the following: Read Control_2b.txt Read Control_3b.txt Error in readGenericHeader(fullname, columns = columns) : Specified column headings not found in file It is like the columns in the file that I gave as input (Control_.txt) are not recognized, maybe I have this problem because is a custom agilent array? If this is the problem, I have to specify in my script the following informations: 1. list with fields R, G, Rb and Gb giving the column names to be used for red and green foreground and background; 2. character vector of names of other columns to be read containing spot-specific information; 3. character vector of names of columns containing annotation information about the probes; Is there someone that can answer me and that has got some experience in the two color agilent custom array analysis? Thank you in advance Giusy _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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