[BioC] xps - error in normalize - "Error: Length of non-varying units is zero."

[Thornton, Matthew]

Hello!

I am trying to optimize my data processing with xps. I am getting an error when using the normalize function. It could be due to improper switches.

here is the error:

> data_norm <- normalize(data_bkgrd, "Normalize_Step2", filedir=outdir, tmpdir="", update = FALSE, select = "pmonly", exonlevel="all", method="mean", option = "transcript:all", logbase = "0", refindex = 0, refmethod = "mean", params = list(0.02, 0), verbose=TRUE)
Opening file </data/met/scmdir/scheme_RaGene20stv1.root> in <READ> mode...
Creating new file </data/met/RA/21July14/strat/Normalize_Step2.root>...
Opening file </data/met/RA/21July14/strat/Background_Step1.root> in <READ> mode...
Preprocessing data using method <preprocess>...
   Normalizing raw data...
      normalizing data using method <mean>...
         filling array <Reference>...
      normalizing <CTR1_Mix2_25Apr14.int>...
      setting selector mask for typepm <16316>
      normalization <Mean>: Scaling factor SF is <0.859736>
      normalizing <CTR2_Mix2_25Apr14.int>...
      setting selector mask for typepm <16316>
Error: Length of non-varying units is zero.
An error has occured: Need to abort current process.
Error in .local(object, ...) : error in rwrapper function ‘Normalize’

Here are the lines in my Rscript for piecewise processing. I am using the default settings but it would be nice to know more about how to optimize them.

# Background correct
data_bkgrd <- bgcorrect(data_raw, "Background_Step1", filedir=outdir, tmpdir="", method="sector", select="pmonly", option="correctbg", params=c(0.02, 4, 4, 0), exonlevel="all", verbose=TRUE)

png(file="Background_Correction_Density_Plot.png", width=600, height=600)
par(mar=c(6,3,1,1));
hist(data_bkgrd, add.legend=TRUE)
dev.off()

# Normalization
data_norm <- normalize(data_bkgrd, "Normalize_Step2", filedir=outdir, tmpdir="", update = FALSE, select = "all", exonlevel="all", method="mean", option = "transcript:all", logbase = "0", refindex = 0, refmethod = "mean", params = list(0.02, 0), verbose=TRUE)

png(file="Normalization_Density_Plot.png", width=600, height=600)
par(mar=c(6,3,1,1));
hist(data_norm, add.legend=TRUE)
dev.off()

# Summarization
data_sum <- summarize(data_norm, "Summary_Step3", filedir=outdir, tmpdir="", update = FALSE, select="pmonly", method = "medianpolish", option = "transcript", exonlevel="core+affx", verbose=TRUE)

png(file="Summary_Density_Plot.png", width=600, height=600)
par(mar=c(6,3,1,1));
hist(data_sum, add.legend=TRUE)
dev.off()

Any comments or advice are greatly appreciated!

Thanks!

Matt


matthew.thornton at med.usc.edu