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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