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Cardinal MSI Help

1–30 of 272

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

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kbemis, … olga.ga...@bostongene.com5

7/24/19

Major update: Cardinal 2.2 released on Bioconductor 3.9

1. Is the dataset in memory? Any of the statistical methods will still always be faster if the data

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Major update: Cardinal 2.2 released on Bioconductor 3.9

1. Is the dataset in memory? Any of the statistical methods will still always be faster if the data

7/24/19

5/17/19

Upcoming Cardinal workshops (2019)

Dear all, We are teaching pre-conference workshops in statistical analysis of MSI experiments using

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Upcoming Cardinal workshops (2019)

Dear all, We are teaching pre-conference workshops in statistical analysis of MSI experiments using

5/17/19

Mar 10

biocparallel error: wrong args for environment subassignment

Hi, I'm using cardinal 3.8 with bpparam <- MulticoreParam(workers=35) register(bpparam) m55657

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biocparallel error: wrong args for environment subassignment

Hi, I'm using cardinal 3.8 with bpparam <- MulticoreParam(workers=35) register(bpparam) m55657

Mar 10

Cardinal MSI Help, kbemis2

9/11/24

IMPORTANT UPDATE: We are migrating to Slack!

Update invitation links can be found by replying to this Github issue: https://github.com/kuwisdelu/

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IMPORTANT UPDATE: We are migrating to Slack!

Update invitation links can be found by replying to this Github issue: https://github.com/kuwisdelu/

9/11/24

Shuo Qian, kbemis5

8/29/24

Combine two MSImagingArrays for further peak alignment

Hi Kylie, I will try what you mentioned, and thanks for your explanation. Best, Shuo 在2024年8月29日星期四

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Combine two MSImagingArrays for further peak alignment

Hi Kylie, I will try what you mentioned, and thanks for your explanation. Best, Shuo 在2024年8月29日星期四

8/29/24

Marco Fidaleo, kbemis2

8/29/24

Different results with spectra and summarizeFeatures

Considering we are talking about (1) an average of intensities versus (2) a distribution of

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Different results with spectra and summarizeFeatures

Considering we are talking about (1) an average of intensities versus (2) a distribution of

8/29/24

Raven Buckman, kbemis5

8/9/24

Segmentation Error After Sub-Setting Pixels

Thanks so much! On Friday, August 9, 2024 at 12:27:53 PM UTC-5 kbemis wrote: Thanks! The error seems

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Segmentation Error After Sub-Setting Pixels

Thanks so much! On Friday, August 9, 2024 at 12:27:53 PM UTC-5 kbemis wrote: Thanks! The error seems

8/9/24

Orotomah Ameh Great, kbemis2

8/9/24

Export image metadata

It sounds like you are trying to export the image data itself, not metadata. Slicing an image as an

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Export image metadata

It sounds like you are trying to export the image data itself, not metadata. Slicing an image as an

8/9/24

aali...@gmail.com, … kbemis6

7/30/24

A couple questions re version 3.6 files and plotting

Hi Matt, It does not support writing multiple intensity channels currently. I am not sure that imzML

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A couple questions re version 3.6 files and plotting

Hi Matt, It does not support writing multiple intensity channels currently. I am not sure that imzML

7/30/24

jennifer.n...@gmail.com, … kbemis10

7/29/24

Exporting Data While Maintaining Clusters

Do you mean plotting the ion image shows a different scale of intensities compared to the mean

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Exporting Data While Maintaining Clusters

Do you mean plotting the ion image shows a different scale of intensities compared to the mean

7/29/24

Даниил Соболев

7/24/24

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,

7/24/24

Даниил Соболев, kbemis2

7/13/24

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

7/13/24

Matthew Smith, kbemis3

6/28/24

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:

6/28/24

Ayush Praveen, kbemis2

6/10/24

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

6/10/24

Marco Fidaleo, Jason Rodencal2

6/6/24

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

6/6/24

Jason Rodencal2

6/5/24

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

6/5/24

Marco Fidaleo, … Matthew Smith3

5/17/24

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

5/17/24

May Institute NEU, kbemis2

5/16/24

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:

5/16/24

Marco Fidaleo, … kbemis13

5/7/24

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

5/7/24

Marco Fidaleo, kbemis11

5/4/24

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

5/4/24

Marco Fidaleo, kbemis2

5/2/24

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.

5/2/24

4/30/24

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

4/30/24

Marina Zavolskova, kbemis2

4/30/24

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

4/30/24

yonghu...@gmail.com, kbemis2

4/10/24

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"

4/10/24

4/1/24

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

4/1/24

3/22/24

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

3/22/24

yonghu...@gmail.com, kbemis2

3/12/24

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

3/12/24

marco.gi...@gmail.com, … kbemis6

3/11/24

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

3/11/24

Davide G. Franchina, … Marco Fidaleo9

3/10/24

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

3/10/24

pips...@gmail.com, … Jimmy Muldoon5

3/9/24

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/

3/9/24

cindy, Giulia Ricciardi4

2/23/24

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

2/23/24

Davide G. Franchina

2/19/24

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 <-

2/19/24

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