Cardinal MSI Help

1–30 of 227

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

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Nadia Atallah, kbemis3

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, kbemis2

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 Saha4

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.com5

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. Franchina4

Mar 22

Hi David, thank you very much, and btw it also works for plot() function Marina суббота, 21 января

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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

Hello, everyone I have a question about peakBin() Here is a spectra of initial data: After such steps

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Hello, everyone I have a question about peakBin() Here is a spectra of initial data: After such steps

Mar 15

Andrew Goodenough, kbemis3

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. Franchina5

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

Hello Cardinal users I am running an experiment consisting of several tissue microarrays and need to

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Hello Cardinal users I am running an experiment consisting of several tissue microarrays and need to

Feb 23

marco.gi...@gmail.com

Feb 13

Hi, do you know the way to perform deisotoping on MSI data? best Marco

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Hi, do you know the way to perform deisotoping on MSI data? best Marco

Feb 13

marco.gi...@gmail.com2

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. Franchina2

Jan 22

Hi Salma, I recently got this error too (it did not happen before). any clue about the solution?

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Hi Salma, I recently got this error too (it did not happen before). any clue about the solution?

Jan 22

Jan 18

Hello everyone, I have some .ibd/.imzML files generated with Shimadzu imzML Converter version 1.21.

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Hello everyone, I have some .ibd/.imzML files generated with Shimadzu imzML Converter version 1.21.

Jan 18

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

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

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

Hi Community, Have you encounter this kind of error when you read MSIdata? If you have the same

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Hi Community, Have you encounter this kind of error when you read MSIdata? If you have the same

11/29/22

Nivedita Bhattacharya, … Pia Hönscheid4

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 Zavolskova5

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

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 Zavolskova2

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, … kbemis6

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 Föll3

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 Föll2

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 Föll4

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 Föll7

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

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

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