Cardinal MSI Help

1–30 of 210

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

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Aug 5

Stitch images side by side

Hi, I am looking to combine imaging mass spec files but want to stitch the images side by side. I

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Stitch images side by side

Hi, I am looking to combine imaging mass spec files but want to stitch the images side by side. I

Aug 5

Adrien Tallois2

Jul 14

Help on some probably basic commands/substracting spectra

I've been steered in the direction of peak picking on a matrix area of the sample with an

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Help on some probably basic commands/substracting spectra

I've been steered in the direction of peak picking on a matrix area of the sample with an

Jul 14

Justin Lin, … kbemis6

Jul 11

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).

Jul 11

Jul 10

Hi group, I am trying to conduct segmentation with spatial shrunken centroids (SSC) however am

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Hi group, I am trying to conduct segmentation with spatial shrunken centroids (SSC) however am

Jul 10

Nadia Atallah, Melanie Föll3

Jul 7

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

Jul 7

Bailey Polimer, Melanie Föll2

Jul 6

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

Jul 6

Shriya Raj, Melanie Föll4

Jul 6

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

Jul 6

Bailey Polimer, … Melanie Föll7

Jun 9

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

Jun 9

Marina Zavolskova

May 4

Hi, everyone Have anybody tried to plot Spatial Shrunken centroids result just for one class? I

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Hi, everyone Have anybody tried to plot Spatial Shrunken centroids result just for one class? I

May 4

Apr 26

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

Apr 26

Marina Zavolskova

Apr 4

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

Apr 4

Xin Ma, … Marina Zavolskova3

Apr 1

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

Apr 1

Daria Emilia, Shad Arf2

Mar 31

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

Mar 31

Marina Zavolskova, kbemis3

Mar 28

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

Mar 28

Mar 10

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.

Mar 10

Theresa Suckert

Mar 4

Combining data - best practice

Hello, I have measurements from ~20 brains (~8 GB) from one experimental cohort. The aim is to

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Combining data - best practice

Hello, I have measurements from ~20 brains (~8 GB) from one experimental cohort. The aim is to

Mar 4

Krista Berlin, … Gordon Luu10

Feb 25

Loading my MSI data sets.

I've never encountered the issue so I don't know if it will help, but maybe try moving the

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Loading my MSI data sets.

I've never encountered the issue so I don't know if it will help, but maybe try moving the

Feb 25

Dmitry Leontyev

Feb 11

How to set conditions with $ such that featureData() has separate columns for the conditions

Hello everyone, I am following the class comparison examples (http://bioconductor.org/packages/

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How to set conditions with $ such that featureData() has separate columns for the conditions

Hello everyone, I am following the class comparison examples (http://bioconductor.org/packages/

Feb 11

Dmitry Leontyev

Feb 9

BiocParallel errors when running crossvalidate()

Hello, *Updated and deleted my previous post on this topic.* I am try to call crossValidate() on my

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BiocParallel errors when running crossvalidate()

Hello, *Updated and deleted my previous post on this topic.* I am try to call crossValidate() on my

Feb 9

Dmitry Leontyev, … educh...@gmail.com16

Feb 9

Z-coordinate Issue and Loading Multiple Runs Into a Single Imaging File

Update: I was able to find the source of the combine() issue. This is because centroided was set to

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Z-coordinate Issue and Loading Multiple Runs Into a Single Imaging File

Update: I was able to find the source of the combine() issue. This is because centroided was set to

Feb 9

Krista Berlin, … Giulia Ricciardi3

Jan 24

Loading MSI data

Hi Krista, as Edu said, I can' see any error either. Your file looks okay and loaded. To check if

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Loading MSI data

Hi Krista, as Edu said, I can' see any error either. Your file looks okay and loaded. To check if

Jan 24

farheen farzana

Jan 11

Request to access cardinal S4 object - MSProcessedImagingExperiment

Hi Kylie When performing Spatially-aware nearest shrunken centroids clustering, please let us know if

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Request to access cardinal S4 object - MSProcessedImagingExperiment

Hi Kylie When performing Spatially-aware nearest shrunken centroids clustering, please let us know if

Jan 11

11/22/21

Cardinal installation in Ubuntu18.04 system

Hello, I am fairly new in R and IMS study. I am having issues installing Cardinal in my Ubuntu 18.04

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Cardinal installation in Ubuntu18.04 system

Hello, I am fairly new in R and IMS study. I am having issues installing Cardinal in my Ubuntu 18.04

11/22/21

Giulia Ricciardi

11/15/21

Problem with normalization by reference feature

Hi everyone, I'm writing because we are experiencing some trouble with the normalize() function.

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Problem with normalization by reference feature

Hi everyone, I'm writing because we are experiencing some trouble with the normalize() function.

11/15/21

Giulia Ricciardi

10/21/21

Error "cannot allocate vector" of a certain size

Hi everyone! I'm processing a centroided "MSProcessedImagingExperiment", with

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Error "cannot allocate vector" of a certain size

Hi everyone! I'm processing a centroided "MSProcessedImagingExperiment", with

10/21/21

Shad Arf, … Gordon Luu8

10/11/21

Problem with assigning experimental runs

Hi all, Regarding the blank/white pixels problem after SSC segmentation, I've confirmed on my

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Problem with assigning experimental runs

Hi all, Regarding the blank/white pixels problem after SSC segmentation, I've confirmed on my

10/11/21

Gordon Luu, Melanie Föll3

10/4/21

Strange spatialShrunkenCentroids results when using imzML converted via Bruker's SCiLS Lab 2020

Hi Gordon, apologies for the late reply and thank you so much for this superb error report! Looking

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Strange spatialShrunkenCentroids results when using imzML converted via Bruker's SCiLS Lab 2020

Hi Gordon, apologies for the late reply and thank you so much for this superb error report! Looking

10/4/21

Nivedita Bhattacharya, … Nivedita Bhattacharya3

7/27/21

Error in valid object

Thank you Kylie for the response, I will run my file through imzMLValidator and get back to you. On

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Error in valid object

Thank you Kylie for the response, I will run my file through imzMLValidator and get back to you. On

7/27/21

Matthew Smith, … Brianna Royer4

7/21/21

Unable to process large MSI object

I too encounter the "attempt to select less than one element in OneIndex" and parallel job

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Unable to process large MSI object

I too encounter the "attempt to select less than one element in OneIndex" and parallel job

7/21/21

Giulia Ricciardi

7/15/21

Extract intensity of mass ranges

Hello everyone, I've recently started working on MSI data and my project requires the extraction

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Extract intensity of mass ranges

Hello everyone, I've recently started working on MSI data and my project requires the extraction

7/15/21

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