[BioC] Question on PROcess package

Farida Mostajabi f0most01 at louisville.edu
Mon Nov 30 21:47:42 CET 2009

To whom it may concern,  

I am a student from University of Louisville, USA. I am currently doing some MALDI-TOF  MS data analysis research
with PROcess package. 

I am trying to use the batch functionality of the package to do pre processing  on 286 spectra. The m/z values 
are not exactly the same throughout the spectra,   which I think it is an assumption in PROcess package.

I used the code below to do  baseline correction for one spectrum  at a time 

B.fs <- list.files(my.B.files, pattern = "\\.*csv\\.*", full.names = TRUE)
nb.file <- length(B.fs)

foo<-lapply(seq(nb.file), function(i) read.files(B.fs[i] ))
f0<-lapply(seq(nb.file), function(i) foo[[i]][foo[[i]][,1]>0,])
basecorr<-lapply(seq(nb.file), function(i)  bslnoff(f0[[i]], method = "loess", bw = 0.1))

I could not use "rmBaseline" function since the row-names of the returning matrix are  the m/z values,  which in my case, are not  identical. 

Would you please give some suggestions on this issue? 

Best Regards, 


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