Data Import and Spectrum Background Subtraction

Skip to first unread message

Xin Ma

Jan 12, 2022, 2:39:53 PM1/12/22
to Cardinal MSI Help
Hi everyone,
I am a new user of Cardinal and R and I have two basic questions related to the package. 
(1) I was trying to import the imzML files to Cardinal and was wondering how I should import more than one files at the same time so that I can load two images for both the diseased and control tissue.
(2) Is there a way to subtract background matrix signals in the mass spectra during the feature selection process?

Hope my questions are clear and thank you so much in advance for any help.


Daria Emilia

Mar 31, 2022, 6:49:10 AM3/31/22
to Cardinal MSI Help
Hi all,

I am also interested to find out more about the background removal feature if one exists :) 

Marina Zavolskova

Apr 1, 2022, 3:44:51 AM4/1/22
to Cardinal MSI Help
Hi everyone, 
I also have the same question about removing background. I started with SpatialShrunkenCentroids() or SpatialKMeans() functions with 2 clusters, so I can extract pixels and features related to either matrix or matrix+sample:
logicvalue <- cluster.file@resultData@listData[[1]]$class[1]==1
file.sample <- file[, logicvalue]
file.matrix <- file[, !logicvalue]
but I don't understand where I can return new intensities meanings.
четверг, 31 марта 2022 г. в 13:49:10 UTC+3,
Reply all
Reply to author
0 new messages