Problem with normalization by reference feature

[Giulia Ricciardi]

Hi everyone,

I’m writing because we are experiencing some trouble with the normalize() function.

Our goal is to normalize by the reference ion m/z 1525.897, which appears like this:

To do so, I am using the following code:

######

data_norm <- normalize(data, method="reference", feature=1525.897,

                            tolerance=5, units="ppm", scale=1)

data_norm <- process(data_norm)

######

 The normalization runs but, at the end of the process, I get this warning message:

“There were 50 or more warnings (use warnings() to see the first 50)”

 

The warnings are all the same:

“Warning messages: reference = 0; values will be set to 0“

 Why do we get this warning? The reference ion is present in all the pixels of the file.

 

When I extract the image of an ion of interest (m/z 1544. 872) before and after normalization I get the following images:

Before normalization:

#####

image(data, mz=1544.872, contrast.enhance="histogram")

#####

 After normalization:

######

image(data_norm, mz=1544.872, contrast.enhance="histogram")

######

 

 

I can't understand where the mistake is.

Thank you to anyone who's willing to help.

Kind regards,

Giulia