[BioC] AgiMicroRna and readMicroRnaFE

[Richard Friedman]

On Aug 28, 2010, at 12:31 PM, Paulo Nuin wrote:

> Hi everyone
>
> I'm trying to read Agilent miRNA data with AgiMicroRna and  
> readMicroRnaFE, but I'm finding an error due to some different  
> column names. My data has this info
>
> miRNA_105_Dec08 (Read Only)	21-Nov-2008 12:14	Agilent Technologies  
> Scanner G2505C US45102857
>
> and the error on the command
>
> dd.micro <- readMicroRnaAFE(targets.micro, verbose = T)
>
> is
>
> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>  Specified column headings not found in file
>
> I dug a bit and found that 3 columns are missing on the input files:
>
> chr_coord
> gBGUsed
> gMeanSignal
>
> My question: is there a workaround this? I don't see column headers  
> that would be similar to the three missing. Can I just change some  
> column names to the ones the function is expecting?
>
> Any help is appreciated.
>
> Thanks in advance
>
> Paulo Nuin
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Paulo,

	I  am not sure  if this is exactly the same problem I had 2 months  
ago, but in case it is I reproduce Pedro
Lopez Romero's reply ro my problem at that time.

#####################################################################################



from: 	plopez at cnic.es
	Subject: 	Re: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse  
miRNA Microarray Release 12.0 G4471A-021828.

	Date: 	June 21, 2010 5:04:25 AM EDT

	To: 	naluru at whoi.edu, bioconductor at stat.math.ethz.ch


Hi Neel and Richard,

Thanks for your patience.



I have slitghtly modified some code in the package, basically related  
to the way read.maimages is used. I have eliminated the use of the  
"chr_coord" column in some of the output files which it was what it  
was causing problems. Before these changes are made effective in the  
library, please, try this temporal solution:



dd=read.maimages(files=targets$FileName,source="agilent",

             columns=list(Rf="gTotalGeneSignal",

                                                         
Gf="gTotalProbeSignal",

                                                         
Rb="gMeanSignal",

                                                         
Gb="gProcessedSignal"),

                            
other.columns=list(IsGeneDetected="gIsGeneDetected",

                                                                        
IsSaturated="gIsSaturated",

                                                                        
IsFeatNonUnifOF="gIsFeatNonUnifOL",

                                                                        
IsFeatPopnOL="gIsFeatPopnOL",

                                                                      
probe_mappings="probe_mappings",

                                                                        
BGKmd="gBGMedianSignal",

                                                                        
BGKus="gBGUsed"),

                             annotation = c( "ControlType",  
"ProbeName","GeneName"),

                             verbose=TRUE,sep="\t",quote="")





before doing anything else, please check first  that you have  
"probe_mappings" in the fifth position of "dd$other"

> names(dd$other)[5]

[1] "probe_mappings"



Then, change the name of "probe_mappings" to the name that AgiMicroRna  
uses for this variable:

> names(dd$other)[5] = "chr_coord"



Then, use the rest of the functions as usual:



ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE)

ddPROC = filterMicroRna(ddTGS.rma,

            dd,

            control = TRUE,

            IsGeneDetected = TRUE,

            wellaboveNEG = FALSE,

            limIsGeneDetected = 50,

            limNEG = 25,

            makePLOT = FALSE,

            targets,

            verbose = TRUE)





Please, let me know if you still have any problem. Thanks



p.-
###################################################################################

I hope this help,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In Memoriam,
George Scithers