staRdom error - Fluorescence data processing

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#1

I am trying to clean up my fluorescence data using staRdom package (script below), but I keep getting this error: Error in eem_raman_normalisation2(eem_list, blank = "Blank_correction") : ***
*** First argument must be of class eemlist, second argument must be 'blank' for a blank correction, a number for correction with this number or a vector with a number for each sample

This script was working perfectly in my previous runs but now it is not working anymore and I don't know what is going on.

I really appreciate your help!

library("staRdom")
cores <- detectCores(logical = FALSE)
folder <- "D:/PhD US/Research/Wetlands/Fall 2023/11082023 Aminoacids/Repetition at lower pH/FL/FL for processing"
eem_list <- eem_read(folder, recursive = TRUE, import_function = eem_csv)
absorbance_path = "D:/PhD US/Research/Wetlands/Fall 2023/11082023 Aminoacids/Repetition at lower pH/UV/Absorbance for processing"
absorbance <- absorbance_read(absorbance_path, cores = cores)
problem <- eem_checkdata(eem_list,absorbance,error=FALSE)
absorbance <- abs_blcor(absorbance,wlrange = c(680,700))
ex_range <- c(210, 300)
em_range <- c(230,350 )
eem_list <- eem_range(eem_list, ex_range, em_range)
eem_list <- eem_extend2largest(eem_list, interpolation = 20, extend = FALSE, cores = cores, resolution = 4)
eem_list <- eem_ife_correction(eem_list,absorbance, cuvl = 1)
eem_list <- eem_remove_blank(eem_list)
eem_list <- eem_raman_normalisation2(eem_list, blank = "Blank_correction")
eem_list <- eem_extract(eem_list, c("nano", "miliq", "milliq", "mq", "Blank"),ignore_case = TRUE)
absorbance <- dplyr::select(absorbance, -matches("nano|miliq|milliq|mq|blank", ignore.case = TRUE))
remove_scatter <- c(TRUE, TRUE, TRUE, TRUE)
remove_scatter_width <- c(50,50,50,50)
eem_list <- eem_rem_scat(eem_list, remove_scatter = remove_scatter, remove_scatter_width = remove_scatter_width)

eem_list <- eem_interp(eem_list, cores = cores, type = 1, extend = FALSE)
eem_overview_plot(eem_list, spp=6, contour = TRUE)

#2

This is the line throwing the error. To see why,

  • First, confirm that eem_list is of class emmlist
  • Second, confirm that Blank_correction is a permissible argument

Details

Possible values for blank:

"blank": normalisation is done with a blank sample. Please refer to eem_raman_normalisation.

numeric: normalisation is done with one value for all samples.

data frame: normalisation is done with different values for different samples. Values are taken from a data.frame with sample names as rownames and one column containing the raman area values.

Blank_correction is given to eem_raman_normalisation2() as a character string, which is none of these.

Rob McCool, one of the team behind Netscape's web server, which eventually became Apache, had as a tagline It was working ten minutes ago, I swear. And it always drives me nuts when it happens to me between repo commits and I have no way to prove to myself that I haven't changed anything. Turns out that I almost always have changed something. When it happens right after ugrading a package, I jump through hoops trying to find how my code was victimized. Breaking changes, however, are much less common than needed to excuse my overlooking my own changes.