Irene Li a écrit :

>Hi bioconductor users,
>
>I am trying to use GLAD to analyze some array CGH data. The code below works 
>for one input file but not for another one in exactly the same format. Does 
>any one know what the error message at the end means?
>  
>
Dear Irene,

The only reason it fails is that there is a value Inf in your LogRatio. 
Thus just replace Inf values by NA before using as.profileCGH.




Please note that there is a new version of the GLAD (Gain and Loss 
Analysis of DNA) package is available at the following URL:

source package:
http://xfer.curie.fr/get/DEurDGQQ7YZ/GLAD_1.1.0.tar.gz

windows package:
http://xfer.curie.fr/get/JKKquwNtKss/GLAD_1.1.0.zip

In this version, a *new function named daglad is available* which allows 
a more efficient and accurate breakpoints detection. A script exemple is 
provided below to show how to use this function. In this new function, 
the user can choose some thesholds to help the algorithm to assign a 
status to each chromosomal region according to its median level :

amplicon: Level (and outliers) with a smoothing value (log-ratio value)
          greater than this threshold are consider as amplicon.

deletion: Level (and outliers) with a smoothing value (log-ratio value)
          lower than this threshold are consider as deletion.

  deltaN: Region with smoothing values in between the interval
          [-deltaN,+deltaN] are supposed to be normal.

 forceGL: Level with smoothing value greater (lower) than 'rangeGL[1]'
          ('rangeGL[2]') are considered as gain (lost).


Please read the pdf vignette for more details.


Should you have any problem in installing or using GLAD, please let us 
know and we will do our best to help you. Any idea of improvement or 
extension or application to other data or problems would also be welcome.

If you are interested in CGH analysis, note that we have also developed 
other tools that will be released soon, in particular:
- MAIA for automatic microarray image analysis
- MANOR for normalisation of microarray data
- VAMP, a java graphical interface for visualisation and analysis of CGH 
profiles.
VAMP can be  requested at vamp@curie.fr MAIA at maia@curie.fr and MANOR 
at manor@curie.fr

A VAMP demo is available at http://bioinfo.curie.fr/vamp (Then click on 
Launch Vamp and File->Import)
Three movies give you an overview of VAMP software capabilities.
        - http://bioinfo-out.curie.fr/tutorial/vamp/vamp-demo1.html
        - http://bioinfo-out.curie.fr/tutorial/vamp/vamp-demo2.html
        - http://bioinfo-out.curie.fr/tutorial/vamp/vamp-demo3.html

We are developing a Web site and have several publications in 
preparation in the field, and if you are interested we will let you know 
when they will be available.

You can visit our Web site at http://bioinfo.curie.fr

Best regards,


>  
>
>>test <- read.table(file="test.txt", skip=1, header=TRUE, sep="\t")
>>profile <- data.frame(LogRatio=log2(test$lym /2), PosOrder=1:dim(test)[1], 
>>PosBase=test$Position, Chromosome=test$Chromosome)
>>dim(profile)
>>    
>>
>[1] 58494     4
>  
>
>>profile[1,]
>>    
>>
>     LogRatio PosOrder  PosBase Chromosome
>1 -0.03690325        1 0.886727          1
>  
>
>>profileCGH <- as.profileCGH(profile)
>>res<- glad(profileCGH)
>>    
>>
>Error in lawsglad(y = subsetdata$LogRatio, hinit = hinit, hmax = hmax,  :
>        NA/NaN/Inf in foreign function call (arg 1)
>
>
>Many thanks.
>
>Irene
>
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>
>
>  
>


-- 
Philippe Hupé
UMR 144 - Service Bioinformatique
Institut Curie
Laboratoire de Transfert (4ème étage)
26 rue d'Ulm
75005 Paris - France
 	
Email :  Philippe.Hupe@curie.fr
Tél :	 +33 (0)1 44 32 42 75
Fax :  	 +33 (0)1 42 34 65 28

website : http://bioinfo.curie.fr


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