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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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Maya Najam
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 Tallois
2
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
, …
kbemis
6
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
Salma Ali
Jul 10
SSC Error
Hi group, I am trying to conduct segmentation with spatial shrunken centroids (SSC) however am
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SSC Error
Hi group, I am trying to conduct segmentation with spatial shrunken centroids (SSC) however am
Jul 10
Nadia Atallah
,
Melanie Föll
3
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 Föll
2
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 Föll
4
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 Föll
7
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
plotting ssc
Hi, everyone Have anybody tried to plot Spatial Shrunken centroids result just for one class? I
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plotting ssc
Hi, everyone Have anybody tried to plot Spatial Shrunken centroids result just for one class? I
May 4
Krista Berlin
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 Zavolskova
3
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 Arf
2
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
,
kbemis
3
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
Krista Berlin
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 Luu
10
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.com
16
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 Ricciardi
3
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
Rana
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 Luu
8
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 Föll
3
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 Bhattacharya
3
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 Royer
4
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