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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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Nadia Atallah
,
kbemis
3
Jun 5
Remote error when running spatialDGMM
Hi Kylie, Thank you for responding! It doesn't look great in my opinion, but I don't know how
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Remote error when running spatialDGMM
Hi Kylie, Thank you for responding! It doesn't look great in my opinion, but I don't know how
Jun 5
K. P. Law
,
kbemis
2
Jun 5
t-SNE, UMAP, dbscan
1. You can always extract the (pxn) data matrix with the spectra() method. You can pass this to any R
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t-SNE, UMAP, dbscan
1. You can always extract the (pxn) data matrix with the spectra() method. You can pass this to any R
Jun 5
pips...@gmail.com
, …
Biju Saha
4
May 15
fatal error: fftw3.h: No such file or directory
Hi Pia, Can you elaborate how you resolved the issue On Thursday, July 9, 2020 at 4:20:30 PM UTC+5:30
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fatal error: fftw3.h: No such file or directory
Hi Pia, Can you elaborate how you resolved the issue On Thursday, July 9, 2020 at 4:20:30 PM UTC+5:30
May 15
Davide G. Franchina
,
educh...@gmail.com
5
Apr 4
spatialShrunkenCentroids not clustering all available pixels?
thank you. but that still does not work. and sorry for the confusion: the second attachment is the
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spatialShrunkenCentroids not clustering all available pixels?
thank you. but that still does not work. and sorry for the confusion: the second attachment is the
Apr 4
Marina Zavolskova
,
Davide G. Franchina
4
Mar 22
plotting ssc
Hi David, thank you very much, and btw it also works for plot() function Marina суббота, 21 января
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plotting ssc
Hi David, thank you very much, and btw it also works for plot() function Marina суббота, 21 января
Mar 22
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
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