Cardinal MSI Help

1–30 of 256

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

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6:04 AM

Cardinal Version 3.6

Hello Everybody, I updated both R (R 4.4.0) and Cardinal (3.6) but I am currently facing some

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Cardinal Version 3.6

Hello Everybody, I updated both R (R 4.4.0) and Cardinal (3.6) but I am currently facing some

6:04 AM

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

Davide G. Franchina, kbemis2

11/16/23

readImzML() Error in if (representation == "centroid spectrum") { : argument is of length zero

Yes, it's a known bug introduced by the recent update. I will push out a fix in the next few days

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readImzML() Error in if (representation == "centroid spectrum") { : argument is of length zero

Yes, it's a known bug introduced by the recent update. I will push out a fix in the next few days

11/16/23

11/14/23

Hello, I have recently started acquiring targeted (MRM) imaging data, but I am unsure how or if this

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Hello, I have recently started acquiring targeted (MRM) imaging data, but I am unsure how or if this

11/14/23

10/16/23

annotation question

Hello, At what step do you recommend annotation? I am assuming that it is best to annotate lipids

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annotation question

Hello, At what step do you recommend annotation? I am assuming that it is best to annotate lipids

10/16/23

Alena Bensussan, Davide G. Franchina3

9/29/23

Visualizing and handling DESI 3D data

Hey David! Thank you for your suggestion! This worked so well, I'm able to visualize my data now.

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Visualizing and handling DESI 3D data

Hey David! Thank you for your suggestion! This worked so well, I'm able to visualize my data now.

9/29/23

yonghu...@gmail.com, kbemis4

9/12/23

A note on plotting speed

Dear Kylie, Thank you very much for your kind help and explanation. It was very helpful! Since you

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A note on plotting speed

Dear Kylie, Thank you very much for your kind help and explanation. It was very helpful! Since you

9/12/23

Nadia Atallah, … kbemis7

9/7/23

regressing out batch effects

Hi Kylie, Thank you - this clears up a lot. The data were indeed from a continuous format imzML. You

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regressing out batch effects

Hi Kylie, Thank you - this clears up a lot. The data were indeed from a continuous format imzML. You

9/7/23

Eduardo Chicano, … jie zh5

8/17/23

Problem loading Bruker exported imzML

My data comes from a Bruker instrument, and I have exported it in .csv format. I building from

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Problem loading Bruker exported imzML

My data comes from a Bruker instrument, and I have exported it in .csv format. I building from

8/17/23

8/17/23

BiocParallel errors

Hello all, I'm encountering an issue while using the `peakBin` function from the Cardinal package

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BiocParallel errors

Hello all, I'm encountering an issue while using the `peakBin` function from the Cardinal package

8/17/23

yonghu...@gmail.com

7/24/23

Is it possible to perform pixel binning?

Hi all, I would like to know if there is an easy way to perform pixel binning using Cardinal? For

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Is it possible to perform pixel binning?

Hi all, I would like to know if there is an easy way to perform pixel binning using Cardinal? For

7/24/23

Salma Ali, … jie zh5

7/17/23

ok,thank you so much!! this is my data and code: https://drive.google.com/file/d/

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ok,thank you so much!! this is my data and code: https://drive.google.com/file/d/

7/17/23

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