Dear list, 

My name is Juan Fernandez-Tajes and I´m trying to use MALDIquant for analysing MS data from ABI 4700 series, I´ve exported a spot set to T2Dextractor in order to convert in mzXML format. I´ve imported this into R with mqReadMzXml function and have followed the suggested flowchart, however when I´m in the step for peak detections I obtained the following error: 

peaks <- detectPeaks(spec, SNR = 2) 
Error en embed(object@intensity, windowSize) : wrong embedding dimension 

Any ideas? 

This is the code I´ve used: 

> library("MALDIquant") 
> library("readMzXmlData") 
> spec <- mqReadMzXml("/Users/juane/XML/") 
> spec <- transformIntensity(prueba, sqrt) 
> movingAverage <- function(y) { return(filter(y, rep(1,5)/5, sides = 2))} 
> spec <- transformIntensity(spec, movingAverage) 
> spec <- removeBaseline(spec, method = "SNIP") 
> peaks <- detectPeaks(spec, SNR = 2) 
Error en embed(object@intensity, windowSize) : wrong embedding dimension 

And this is my session.Info 

R version 2.15.1 (2012-06-22) 
Platform: i386-apple-darwin9.8.0/i386 (32-bit) 

locale: 
[1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 

attached base packages: 
[1] stats graphics grDevices utils datasets methods base 

other attached packages: 
[1] readMzXmlData_2.3 XML_3.9-4 digest_0.5.2 bitops_1.0-4.1 MALDIquant_1.2 


Many thanks in advance 

Juan 

--------------------------------------------------------------- 
Juan Fernandez Tajes, ph. D 
Grupo XENOMAR 
Departamento de Biología Celular y Molecular 
Facultad de Ciencias-Universidade da Coruña 
Tlf. +34 981 167000 ext 2030 
e-mail: jfernandezt@udc.es 
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