[BioC] Question on PROcess package
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?
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