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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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Nay Min Min Thaw Saw
Mar 17
Position, subscript out of bounds , image causing crashes
Hello everyone, I am encountering some problems while processing image files with Cardinal. Could you
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Position, subscript out of bounds , image causing crashes
Hello everyone, I am encountering some problems while processing image files with Cardinal. Could you
Mar 17
Marina Zavolskova
Mar 15
peakBin
Hello, everyone I have a question about peakBin() Here is a spectra of initial data: After such steps
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peakBin
Hello, everyone I have a question about peakBin() Here is a spectra of initial data: After such steps
Mar 15
Andrew Goodenough
,
kbemis
3
Mar 10
mzAlign causing crashes
Hi Kylie, peakBin() also fails on those same pixels. Some more information on the image: it is from a
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mzAlign causing crashes
Hi Kylie, peakBin() also fails on those same pixels. Some more information on the image: it is from a
Mar 10
Maya Najam
, …
Davide G. Franchina
5
Mar 3
Stitch images side by side
Hi all, please see https://github.com/kuwisdelu/Cardinal/issues/24 for a temporary solution to cbind(
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Stitch images side by side
Hi all, please see https://github.com/kuwisdelu/Cardinal/issues/24 for a temporary solution to cbind(
Mar 3
Andreas Abildskov
Feb 23
SelectROI()
Hello Cardinal users I am running an experiment consisting of several tissue microarrays and need to
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SelectROI()
Hello Cardinal users I am running an experiment consisting of several tissue microarrays and need to
Feb 23
marco.gi...@gmail.com
Feb 13
deisotoping
Hi, do you know the way to perform deisotoping on MSI data? best Marco
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deisotoping
Hi, do you know the way to perform deisotoping on MSI data? best Marco
Feb 13
marco.gi...@gmail.com
2
Feb 9
selectROI: wrong position
the problem has been solved... it was a problem regarding the resolution of my display. The display
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selectROI: wrong position
the problem has been solved... it was a problem regarding the resolution of my display. The display
Feb 9
Salma Ali
,
Davide G. Franchina
2
Jan 22
SSC Error
Hi Salma, I recently got this error too (it did not happen before). any clue about the solution?
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SSC Error
Hi Salma, I recently got this error too (it did not happen before). any clue about the solution?
Jan 22
Marina Zavolskova
,
Davide G. Franchina
3
Jan 20
plotting ssc
Hi Marina, here is is what I finally came up with to plot the result of just one class after SSC:
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plotting ssc
Hi Marina, here is is what I finally came up with to plot the result of just one class after SSC:
Jan 20
Lutz Freytag
Jan 18
Shimazdu
Hello everyone, I have some .ibd/.imzML files generated with Shimadzu imzML Converter version 1.21.
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Shimazdu
Hello everyone, I have some .ibd/.imzML files generated with Shimadzu imzML Converter version 1.21.
Jan 18
Lutz Freytag
12/23/22
Normalization - error in reducer$value.cache[[
Hi everyone, by trying to normalize my data an error occurs see screenshot_1 Last time I have run
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Normalization - error in reducer$value.cache[[
Hi everyone, by trying to normalize my data an error occurs see screenshot_1 Last time I have run
12/23/22
Dan
12/14/22
Matrix peak subtraction
Hello everyone, Relatively new to Cardinal and R in general and I was wondering if there are specific
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Matrix peak subtraction
Hello everyone, Relatively new to Cardinal and R in general and I was wondering if there are specific
12/14/22
Dan
12/14/22
Matrix peak subtraction
Hello everyone, Relatively new to Cardinal and R in general and I was wondering if there are specific
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Matrix peak subtraction
Hello everyone, Relatively new to Cardinal and R in general and I was wondering if there are specific
12/14/22
Miao YU (yufree)
12/7/22
spatial shrunken centroids for high resolution data
Hi Community, Thanks for this useful software! I am dealing with a high resolution MS imaging with
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spatial shrunken centroids for high resolution data
Hi Community, Thanks for this useful software! I am dealing with a high resolution MS imaging with
12/7/22
Nay Min Min Thaw Saw
11/29/22
Error unlist
Hi Community, Have you encounter this kind of error when you read MSIdata? If you have the same
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Error unlist
Hi Community, Have you encounter this kind of error when you read MSIdata? If you have the same
11/29/22
Nivedita Bhattacharya
, …
Pia Hönscheid
4
10/28/22
Error in valid object
Dear Kylie, can you give us some update about the issue : Error in validObject(x): invalid class
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Error in valid object
Dear Kylie, can you give us some update about the issue : Error in validObject(x): invalid class
10/28/22
Davide G. Franchina
,
Marina Zavolskova
5
9/19/22
Possible bias due to matrix distribution in unsupervised analysis?
Hi, yes! thanks. In my case your code worked after setting the rows of df_file_ssc_5 to the actual mz
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Possible bias due to matrix distribution in unsupervised analysis?
Hi, yes! thanks. In my case your code worked after setting the rows of df_file_ssc_5 to the actual mz
9/19/22
Lutz Freytag
9/7/22
misalignment selectROI()
Hi, everyone. I´m new to Cardinal. I have a test data set > test_profile An object of class '
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misalignment selectROI()
Hi, everyone. I´m new to Cardinal. I have a test data set > test_profile An object of class '
9/7/22
Marina Zavolskova
2
9/7/22
legend font size
If I try image(file, mz = 813, cex.axis = 2) I change both legend size, and axis: it doesn't look
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legend font size
If I try image(file, mz = 813, cex.axis = 2) I change both legend size, and axis: it doesn't look
9/7/22
Justin Lin
, …
kbemis
6
7/11/22
Processing/Normalization Speed Optimization
Hello Dr. Bemis, Seems like an I/O issue was indeed the case (I accessed the data through NAS).
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Processing/Normalization Speed Optimization
Hello Dr. Bemis, Seems like an I/O issue was indeed the case (I accessed the data through NAS).
7/11/22
Nadia Atallah
,
Melanie Föll
3
7/7/22
combining different runs with different numbers of features
Hi Melanie, Thanks for your response. The MSI data is of the "processed" type for each of
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combining different runs with different numbers of features
Hi Melanie, Thanks for your response. The MSI data is of the "processed" type for each of
7/7/22
Bailey Polimer
,
Melanie Föll
2
7/6/22
Combine function error
Hi Bailey, the problem might be that you did not specify the resolution, which means that the optimal
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Combine function error
Hi Bailey, the problem might be that you did not specify the resolution, which means that the optimal
7/6/22
Shriya Raj
,
Melanie Föll
4
7/6/22
Access Raw Data
Dear Shriya, yes with spectra() or iData() you obtain a table in which each line is one mz feature
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Access Raw Data
Dear Shriya, yes with spectra() or iData() you obtain a table in which each line is one mz feature
7/6/22
Bailey Polimer
, …
Melanie Föll
7
6/9/22
Cardinal not reading file
Oh ok that worked! Thank you so much! On Thursday, 9 June 2022 at 04:12:38 UTC-4 foellm...@gmail.com
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Cardinal not reading file
Oh ok that worked! Thank you so much! On Thursday, 9 June 2022 at 04:12:38 UTC-4 foellm...@gmail.com
6/9/22
Krista Berlin
4/26/22
Combining Multiple data files
I am trying to combine three large imaging files. When loaded into R, two of the files read as
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Combining Multiple data files
I am trying to combine three large imaging files. When loaded into R, two of the files read as
4/26/22
Marina Zavolskova
4/4/22
intensities subtracting
Hi everyone, In searching of the best way to remove matrix influence i decided to subtract mean
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intensities subtracting
Hi everyone, In searching of the best way to remove matrix influence i decided to subtract mean
4/4/22
Xin Ma
, …
Marina Zavolskova
3
4/1/22
Data Import and Spectrum Background Subtraction
Hi everyone, I also have the same question about removing background. I started with
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Data Import and Spectrum Background Subtraction
Hi everyone, I also have the same question about removing background. I started with
4/1/22
Daria Emilia
,
Shad Arf
2
3/31/22
When loading in the data the number of features is a 100 fold less than expected
Hi Daria, I can recommend two things. 1) Generate a minimal reproducible example so that one can
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When loading in the data the number of features is a 100 fold less than expected
Hi Daria, I can recommend two things. 1) Generate a minimal reproducible example so that one can
3/31/22
Marina Zavolskova
,
kbemis
3
3/28/22
Peak Filtering and Peak comparing
Hi Kylie, Thank you very much for your reply, now it works works as intended! About comparing peak
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Peak Filtering and Peak comparing
Hi Kylie, Thank you very much for your reply, now it works works as intended! About comparing peak
3/28/22
Krista Berlin
3/10/22
Combined Data Mean Spectrum Error
Cardinal MSI Help Group, I have combined three MSI data sets with defined mass range and resolution.
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Combined Data Mean Spectrum Error
Cardinal MSI Help Group, I have combined three MSI data sets with defined mass range and resolution.
3/10/22