Cardinal MSI Help

1–30 of 188

Welcome to the help group for Cardinal, an R toolbox for statistical analysis of mass spectrometry imaging experiments.

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Nov 22

Cardinal installation in Ubuntu18.04 system

Hello, I am fairly new in R and IMS study. I am having issues installing Cardinal in my Ubuntu 18.04

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Cardinal installation in Ubuntu18.04 system

Hello, I am fairly new in R and IMS study. I am having issues installing Cardinal in my Ubuntu 18.04

Nov 22

Giulia Ricciardi

Nov 15

Problem with normalization by reference feature

Hi everyone, I'm writing because we are experiencing some trouble with the normalize() function.

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Problem with normalization by reference feature

Hi everyone, I'm writing because we are experiencing some trouble with the normalize() function.

Nov 15

Giulia Ricciardi

Oct 21

Error "cannot allocate vector" of a certain size

Hi everyone! I'm processing a centroided "MSProcessedImagingExperiment", with

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Error "cannot allocate vector" of a certain size

Hi everyone! I'm processing a centroided "MSProcessedImagingExperiment", with

Oct 21

Shad Arf, … Gordon Luu8

Oct 11

Problem with assigning experimental runs

Hi all, Regarding the blank/white pixels problem after SSC segmentation, I've confirmed on my

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Problem with assigning experimental runs

Hi all, Regarding the blank/white pixels problem after SSC segmentation, I've confirmed on my

Oct 11

Gordon Luu, Melanie Föll3

Oct 4

Strange spatialShrunkenCentroids results when using imzML converted via Bruker's SCiLS Lab 2020

Hi Gordon, apologies for the late reply and thank you so much for this superb error report! Looking

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Strange spatialShrunkenCentroids results when using imzML converted via Bruker's SCiLS Lab 2020

Hi Gordon, apologies for the late reply and thank you so much for this superb error report! Looking

Oct 4

Nivedita Bhattacharya, … Nivedita Bhattacharya3

Jul 27

Error in valid object

Thank you Kylie for the response, I will run my file through imzMLValidator and get back to you. On

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Error in valid object

Thank you Kylie for the response, I will run my file through imzMLValidator and get back to you. On

Jul 27

Matthew Smith, … Brianna Royer4

Jul 21

Unable to process large MSI object

I too encounter the "attempt to select less than one element in OneIndex" and parallel job

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Unable to process large MSI object

I too encounter the "attempt to select less than one element in OneIndex" and parallel job

Jul 21

Giulia Ricciardi

Jul 15

Extract intensity of mass ranges

Hello everyone, I've recently started working on MSI data and my project requires the extraction

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Extract intensity of mass ranges

Hello everyone, I've recently started working on MSI data and my project requires the extraction

Jul 15

Andreas Abildskov, Melanie Föll2

Jun 23

Manual CV-folds

Hi Andreas, the .fold argument needs a factor as input that specifies the a fold for each spectrum.

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Manual CV-folds

Hi Andreas, the .fold argument needs a factor as input that specifies the a fold for each spectrum.

Jun 23

luna maria Munoz, … Groupe Chaurand3

Jun 14

Normlaization problem

Hi Melanie, I still have a couple of issues with the normalization feature: before normalization my

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Normlaization problem

Hi Melanie, I still have a couple of issues with the normalization feature: before normalization my

Jun 14

ismaelu...@gmail.com

Jun 3

Error in method kmeans using a Shiny UI

Hi all, I am making a small Shiny interface for an image analysis workflow in MALDI Imaging. I have a

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Error in method kmeans using a Shiny UI

Hi all, I am making a small Shiny interface for an image analysis workflow in MALDI Imaging. I have a

Jun 3

Pascal Egner, Melanie Föll4

May 28

spatialShrunkenCentroids predict not working

Hi Pascal, great to hear that you found a solution and thanks a lot for sharing it here! Melanie

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spatialShrunkenCentroids predict not working

Hi Pascal, great to hear that you found a solution and thanks a lot for sharing it here! Melanie

May 28

Matthew Smith, Melanie Föll4

May 24

I fixed this issue - it was more related to the HPC system. On Wednesday, May 19, 2021 at 5:42:52 PM

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I fixed this issue - it was more related to the HPC system. On Wednesday, May 19, 2021 at 5:42:52 PM

May 24

Andreas Abildskov2

May 23

Extracting values for factor levels

I found the way to do it. torsdag den 20. maj 2021 kl. 18.51.37 UTC+2 skrev Andreas Abildskov: Hi, I

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Extracting values for factor levels

I found the way to do it. torsdag den 20. maj 2021 kl. 18.51.37 UTC+2 skrev Andreas Abildskov: Hi, I

May 23

Matthew Smith, Ethan Yang3

May 12

Multiple subsets

Thanks for your reply - I have now started using this approach as I find storing all the ROIs in the

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Multiple subsets

Thanks for your reply - I have now started using this approach as I find storing all the ROIs in the

May 12

gawrile...@gmail.com, Melanie Föll2

Apr 9

Hi Olga, happy to hear that it is useful for you. Recalibration is still in beta version but should

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Hi Olga, happy to hear that it is useful for you. Recalibration is still in beta version but should

Apr 9

Mar 17

Set up data from multiple tissues for Group means-based testing

Hello, I have a query about how to set up data for Group means-based testing. I have 6 individual

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Set up data from multiple tissues for Group means-based testing

Hello, I have a query about how to set up data for Group means-based testing. I have 6 individual

Mar 17

Ethan Yang, … ismaelu...@gmail.com11

Mar 15

mzAlign vs PeakAlign

So much thank you Melani, that was our problem. When we proved it my computer don't have the

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mzAlign vs PeakAlign

So much thank you Melani, that was our problem. When we proved it my computer don't have the

Mar 15

baina....@gmail.com

Mar 12

how to import list of imzml files

Dear Kylie, dear all, I imported an Analyze file and exported IMZML files by MALDIquant Foreign. It

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how to import list of imzml files

Dear Kylie, dear all, I imported an Analyze file and exported IMZML files by MALDIquant Foreign. It

Mar 12

Feb 16

how to configure parallelism?

Hi, Recently, I get an error after running cardinal in our server saying 'Cannot allocate memory

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how to configure parallelism?

Hi, Recently, I get an error after running cardinal in our server saying 'Cannot allocate memory

Feb 16

yonghu...@gmail.com, Melanie Föll5

Feb 11

number of mass features and the resolution of binning

Dear Melanie, Thanks a lot for your help. I am used to work with the MSI data generated using

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number of mass features and the resolution of binning

Dear Melanie, Thanks a lot for your help. I am used to work with the MSI data generated using

Feb 11

baina....@gmail.com, kbemis2

Feb 2

Ion image 1:1 export

I would suggest using slice() to get a matrix/array of intensity values. You can coerce this to a

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Ion image 1:1 export

I would suggest using slice() to get a matrix/array of intensity values. You can coerce this to a

Feb 2

Olga Gavrilenko, … Olga Vitek5

12/18/20

t-statistics in the topLabels of Spatial Shrunken centroids

Dear Noel: with the t-statistics, the important aspect is not the sign but the magnitude of the

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t-statistics in the topLabels of Spatial Shrunken centroids

Dear Noel: with the t-statistics, the important aspect is not the sign but the magnitude of the

12/18/20

Sandra Murphy, foellm...@gmail.com5

11/27/20

Problem combining imaging runs after mzBin

Hi Melanie, I just realised I made a stupid error and didn't name the result of process(), so

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Problem combining imaging runs after mzBin

Hi Melanie, I just realised I made a stupid error and didn't name the result of process(), so

11/27/20

Marie Gorka, foellm...@gmail.com4

11/25/20

Extract intensity from a predefined m/z list

Hi Marie, please make sure that you use Cardinal version 2.6 or higher and that your single files are

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Extract intensity from a predefined m/z list

Hi Marie, please make sure that you use Cardinal version 2.6 or higher and that your single files are

11/25/20

Sandra Murphy, foellm...@gmail.com3

11/24/20

Label separate runs as disease/control to create diagnosis for class comparison

Hi Melanie, Thanks so much for your help and example code- that's really useful! Really

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Label separate runs as disease/control to create diagnosis for class comparison

Hi Melanie, Thanks so much for your help and example code- that's really useful! Really

11/24/20

Hu, foellm...@gmail.com2

11/24/20

subset MSImagingExperiment object

Hi Hu, your code is all fine, the only problem is that there is no intensity above 300: range(Int1200

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subset MSImagingExperiment object

Hi Hu, your code is all fine, the only problem is that there is no intensity above 300: range(Int1200

11/24/20

Matthew Smith, foellm...@gmail.com2

11/24/20

Combining imaging objects

Hi Matt, the peakBin works as follows: it takes spectra in profile mode and for each provided

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Combining imaging objects

Hi Matt, the peakBin works as follows: it takes spectra in profile mode and for each provided

11/24/20

Sandra Murphy, kbemis3

11/10/20

centroided NA cannot combine imzML files

That was embarrassingly easy to fix! Thank you so much for your quick response and help- my files

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centroided NA cannot combine imzML files

That was embarrassingly easy to fix! Thank you so much for your quick response and help- my files

11/10/20

10/27/20

Possibility to customise intensity scale

Hi all, I would like to compare the distribution and relative abundance of one molecules from two

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Possibility to customise intensity scale

Hi all, I would like to compare the distribution and relative abundance of one molecules from two

10/27/20

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