Cardinal MSI Help

1–30 of 266

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

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aali...@gmail.com, … Matthew Smith5

Jul 24

A couple questions re version 3.6 files and plotting

This is a great feature that I hadn't realised. Does it also enable saving multiple spectraData()

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A couple questions re version 3.6 files and plotting

This is a great feature that I hadn't realised. Does it also enable saving multiple spectraData()

Jul 24

Даниил Соболев

Jul 24

Unavailability of the mz removal in new version.

Dear Dr. Kylie Ariel Bemis, Recently, I tried to remove certain mz values from my dataset. However,

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Unavailability of the mz removal in new version.

Dear Dr. Kylie Ariel Bemis, Recently, I tried to remove certain mz values from my dataset. However,

Jul 24

Даниил Соболев, kbemis2

Jul 13

Plotting Different Smoothing Algorithms

The issue seems to be the processed plot is ignoring the dataset's pixel names. I am working on a

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Plotting Different Smoothing Algorithms

The issue seems to be the processed plot is ignoring the dataset's pixel names. I am working on a

Jul 13

Matthew Smith, kbemis3

Jun 28

Visualise ROI masks in v3.6

Perfect, that has resolved it. Thanks :) On Thursday, June 27, 2024 at 8:10:37 PM UTC+2 kbemis wrote:

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Visualise ROI masks in v3.6

Perfect, that has resolved it. Thanks :) On Thursday, June 27, 2024 at 8:10:37 PM UTC+2 kbemis wrote:

Jun 28

Ayush Praveen, kbemis2

Jun 10

sgmixn issue while running SpatialDGMM

This is fixed now. May take a couple days to appear on Bioconductor. If you need a fix sooner and

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sgmixn issue while running SpatialDGMM

This is fixed now. May take a couple days to appear on Bioconductor. If you need a fix sooner and

Jun 10

Marco Fidaleo, Jason Rodencal2

Jun 6

Identification of m/z differences in 2 different ROI

Hello! You can select ROIs in cardinal datasets in Cardinal v3.6. Then, it is fairly simple to assign

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Identification of m/z differences in 2 different ROI

Hello! You can select ROIs in cardinal datasets in Cardinal v3.6. Then, it is fairly simple to assign

Jun 6

Jason Rodencal2

Jun 5

Converting RDS to cardinal object

I managed to figure out conversion of the .RDS to Cardinal using this very helpful video posted

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Converting RDS to cardinal object

I managed to figure out conversion of the .RDS to Cardinal using this very helpful video posted

Jun 5

Marco Fidaleo, … Matthew Smith3

May 17

How to use .mzML files or to convert them into .imzML and .ibd

Hello, I too ran into this problem with targeted MSI analysis with Waters. As a temporary fix until

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How to use .mzML files or to convert them into .imzML and .ibd

Hello, I too ran into this problem with targeted MSI analysis with Waters. As a temporary fix until

May 17

May Institute NEU, kbemis2

May 16

Cardinal short course session in May Institute 2024 at Northeastern University

Thank you, Sai! -Kylie On Thursday, May 16, 2024 at 3:32:52 PM UTC-6 mayinsti...@gmail.com wrote:

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Cardinal short course session in May Institute 2024 at Northeastern University

Thank you, Sai! -Kylie On Thursday, May 16, 2024 at 3:32:52 PM UTC-6 mayinsti...@gmail.com wrote:

May 16

Marco Fidaleo, … kbemis13

May 7

Errore in get_matter_list_sublist(x, i, j) : failed to read data elements

Yes, the imzML offsets are telling Cardinal to load spectra that don't exist in the ibd file, so

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Errore in get_matter_list_sublist(x, i, j) : failed to read data elements

Yes, the imzML offsets are telling Cardinal to load spectra that don't exist in the ibd file, so

May 7

Marco Fidaleo, kbemis11

May 4

Cardinal Version 3.6

Thanks Kylie, very clear, as usual! Best, M Il giorno sabato 4 maggio 2024 alle 19:04:58 UTC+2 kbemis

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Cardinal Version 3.6

Thanks Kylie, very clear, as usual! Best, M Il giorno sabato 4 maggio 2024 alle 19:04:58 UTC+2 kbemis

May 4

Marco Fidaleo, kbemis2

May 2

How to focus on a specific class of molecules

You are using s=0, so there is no sparsity enforced, so all clusters will be informed by all ions.

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How to focus on a specific class of molecules

You are using s=0, so there is no sparsity enforced, so all clusters will be informed by all ions.

May 2

Apr 30

Cardinal 3.6 -- major update with breaking changes

Dear all, Cardinal 3.6 should be released tomorrow. This is a major update with some breaking changes

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Cardinal 3.6 -- major update with breaking changes

Dear all, Cardinal 3.6 should be released tomorrow. This is a major update with some breaking changes

Apr 30

Marina Zavolskova, kbemis2

Apr 30

Not directly without some additional calculations. One way I can think of would be to use the

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Not directly without some additional calculations. One way I can think of would be to use the

Apr 30

yonghu...@gmail.com, kbemis2

Apr 10

How to combine multiple MSI datasets acquired in centroid mode?

It isn't exactly a bug. It is because if centroided peaks are stored in "processed"

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How to combine multiple MSI datasets acquired in centroid mode?

It isn't exactly a bug. It is because if centroided peaks are stored in "processed"

Apr 10

Apr 1

a possible bug in `subset` function

Dear Cardinal developers, I hope this message finds you well. I am writing to bring to your attention

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a possible bug in `subset` function

Dear Cardinal developers, I hope this message finds you well. I am writing to bring to your attention

Apr 1

Mar 22

Failure to plot high resolution images

Hello, Love using this package, such flexibility and functionality. I have started to encounter a

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Failure to plot high resolution images

Hello, Love using this package, such flexibility and functionality. I have started to encounter a

Mar 22

yonghu...@gmail.com, kbemis2

Mar 12

Release of ShinyCardinal, a GUI version of Cardinal

Cool! -Kylie On Tuesday, March 12, 2024 at 11:33:57 AM UTC-4 yonghu...@gmail.com wrote: Dear Cardinal

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Release of ShinyCardinal, a GUI version of Cardinal

Cool! -Kylie On Tuesday, March 12, 2024 at 11:33:57 AM UTC-4 yonghu...@gmail.com wrote: Dear Cardinal

Mar 12

marco.gi...@gmail.com, … kbemis6

Mar 11

removing matrix regions from dataset

Thanks for bringing this one to my attention with an example. It took a little investigating, but a

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removing matrix regions from dataset

Thanks for bringing this one to my attention with an example. It took a little investigating, but a

Mar 11

Davide G. Franchina, … Marco Fidaleo9

Mar 10

image(ssc) returns no image

Thank you, Kylie! It worked perfectly! Cheers, M Il giorno domenica 10 marzo 2024 alle 17:48:23 UTC+1

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image(ssc) returns no image

Thank you, Kylie! It worked perfectly! Cheers, M Il giorno domenica 10 marzo 2024 alle 17:48:23 UTC+1

Mar 10

pips...@gmail.com, … Jimmy Muldoon5

Mar 9

fatal error: fftw3.h: No such file or directory

Hi all Had a similar issue, Cardinal installation failing on linux with cc -I"/usr/share/R/

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fatal error: fftw3.h: No such file or directory

Hi all Had a similar issue, Cardinal installation failing on linux with cc -I"/usr/share/R/

Mar 9

cindy, Giulia Ricciardi4

Feb 23

Error when loading my data

Hello! I'm not sure about what could be the issue here. Maybe you can try to convert your data

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Error when loading my data

Hello! I'm not sure about what could be the issue here. Maybe you can try to convert your data

Feb 23

Davide G. Franchina

Feb 19

cannot create MSImagingExperiment()

Hi all, I am trying to create an MSImagingExperiment from scratch but I get this error: object <-

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cannot create MSImagingExperiment()

Hi all, I am trying to create an MSImagingExperiment from scratch but I get this error: object <-

Feb 19

Feb 12

coregistration of optical images

Hi, has the co-registration for the optical images been implemented yet? I am looking for a way to

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coregistration of optical images

Hi, has the co-registration for the optical images been implemented yet? I am looking for a way to

Feb 12

Софья Гуринова

Feb 8

Hello, I have a question about peakAlign function. Me and my colleague used the same file for

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Hello, I have a question about peakAlign function. Me and my colleague used the same file for

Feb 8

Jan 28

April 29 – May 10, 2024: May Institute on computation and statistics for mass spectrometry and proteomics

Dear friends and colleagues: The May Institute on Computation and Statistics for Mass Spectrometry

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April 29 – May 10, 2024: May Institute on computation and statistics for mass spectrometry and proteomics

Dear friends and colleagues: The May Institute on Computation and Statistics for Mass Spectrometry

Jan 28

Davide G. Franchina, Kajal Gupta2

Jan 19

Cardinal imzML compatibility with MZmine

Hi Did it work for you afterwards? Thanks On Saturday 21 October 2023 at 20:50:53 UTC-2:30 davidef...

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Cardinal imzML compatibility with MZmine

Hi Did it work for you afterwards? Thanks On Saturday 21 October 2023 at 20:50:53 UTC-2:30 davidef...

Jan 19

Jan 17

Generating ion images - "R encountered a fatal error"

In case anyone experiences a similar issue, I found out this was related to the memory available on

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Generating ion images - "R encountered a fatal error"

In case anyone experiences a similar issue, I found out this was related to the memory available on

Jan 17

yonghu...@gmail.com, kbemis5

11/22/23

How to increase the number of reference peaks during MSI data processing?

Thanks. Looks like this was an unintended side-effect to changes in how the default reference peaks

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How to increase the number of reference peaks during MSI data processing?

Thanks. Looks like this was an unintended side-effect to changes in how the default reference peaks

11/22/23

marco.gi...@gmail.com, … kbemis5

11/22/23

selectROI: wrong position

Yes, it is an issue with the RStudio graphics device; its coordinates can be sensitive to zooming and

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selectROI: wrong position

Yes, it is an issue with the RStudio graphics device; its coordinates can be sensitive to zooming and

11/22/23

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