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Cardinal MSI Help
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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 Smith
5
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
,
kbemis
2
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
,
kbemis
3
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
,
kbemis
2
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 Rodencal
2
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 Rodencal
2
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 Smith
3
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
,
kbemis
2
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
, …
kbemis
13
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
,
kbemis
11
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
,
kbemis
2
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
kbemis
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
,
kbemis
2
Apr 30
Select pixels
Not directly without some additional calculations. One way I can think of would be to use the
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Select pixels
Not directly without some additional calculations. One way I can think of would be to use the
Apr 30
yonghu...@gmail.com
,
kbemis
2
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
Zhengnan Cheng
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
Matthew Smith
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
,
kbemis
2
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
, …
kbemis
6
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 Fidaleo
9
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 Muldoon
5
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 Ricciardi
4
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
Marco Vicari
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
peakAlign
Hello, I have a question about peakAlign function. Me and my colleague used the same file for
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peakAlign
Hello, I have a question about peakAlign function. Me and my colleague used the same file for
Feb 8
vitek.olga
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 Gupta
2
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
Matthew Smith
2
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
,
kbemis
5
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
, …
kbemis
5
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