'Error in corcut' after full CoGAPS run

[parkerstevenson]

As my 3-hour CoGAPS run finished up, the following error appeared:

Matching Patterns Across Subsets...
Error in corcut(allPatterns, gapsParams@cut, gapsParams@minNS) : 
  NA values in correlation of patterns
In addition: Warning messages:
1: In checkInputs(data, uncertainty, allParams) :
  running distributed cogaps without mtx/tsv/csv/gct data
2: In cor(allPatterns) : the standard deviation is zero

Is there a way to export part of the CoGAPS result during the run, so that the result isn't lost if this occurs?

[ejfertig]

It’s hard to know without more information about your data why this is happening. Do any of your genes or cells have zero variance or zero expression across the board?

Elana J. Fertig, PhD, FAIMBE Division Director and Associate Cancer Center Director of Quantitative Sciences co-Director Convergence Institute co-Director Single-Cell Training and Analysis Center (STAC) Daniel Nathans Scientific Innovator Professor of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics Johns Hopkins University https://fertiglab.comhttps://fertiglab.com/ @FertigLab

On Jun 6, 2023, at 9:46 AM, parkerstevenson @.**@.>> wrote:

As my 3-hour CoGAPS run finished up, the following error appeared:

Matching Patterns Across Subsets... Error in corcut(allPatterns, @., @.) : NA values in correlation of patterns In addition: Warning messages: 1: In checkInputs(data, uncertainty, allParams) : running distributed cogaps without mtx/tsv/csv/gct data 2: In cor(allPatterns) : the standard deviation is zero

— Reply to this email directly, view it on GitHubhttps://github.com/FertigLab/CoGAPS/issues/71, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AATMMK52XENIUABRS5WSJMTXJ4YFHANCNFSM6AAAAAAY4OHOOA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[parkerstevenson]

I removed the genes with zero expression across the board, and the cells were pre-filtered by my collaborator so there shouldn't be zero variance/expression there either.

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From: Elana J Fertig @.> Sent: Tuesday, June 6, 2023 9:48:51 AM To: FertigLab/CoGAPS @.> Cc: Parker Stevenson @.>; Author @.> Subject: Re: [FertigLab/CoGAPS] 'Error in corcut' after full CoGAPS run (Issue #71)

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It’s hard to know without more information about your data why this is happening. Do any of your genes or cells have zero variance or zero expression across the board?

Elana J. Fertig, PhD, FAIMBE Division Director and Associate Cancer Center Director of Quantitative Sciences co-Director Convergence Institute co-Director Single-Cell Training and Analysis Center (STAC) Daniel Nathans Scientific Innovator Professor of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics Johns Hopkins University https://fertiglab.comhttps://fertiglab.com/ @FertigLab

On Jun 6, 2023, at 9:46 AM, parkerstevenson @.**@.>> wrote:

As my 3-hour CoGAPS run finished up, the following error appeared:

Matching Patterns Across Subsets... Error in corcut(allPatterns, @., @.) : NA values in correlation of patterns In addition: Warning messages: 1: In checkInputs(data, uncertainty, allParams) : running distributed cogaps without mtx/tsv/csv/gct data 2: In cor(allPatterns) : the standard deviation is zero

— Reply to this email directly, view it on GitHubhttps://github.com/FertigLab/CoGAPS/issues/71, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AATMMK52XENIUABRS5WSJMTXJ4YFHANCNFSM6AAAAAAY4OHOOA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/FertigLab/CoGAPS/issues/71#issuecomment-1578805573, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BALECGPLA2EH3DC75EJT65DXJ4YMHANCNFSM6AAAAAAY4OHOOA. You are receiving this because you authored the thread.Message ID: @.***>

[dimalvovs]

I removed the genes with zero expression across the board, and the cells were pre-filtered by my collaborator so there shouldn't be zero variance/expression there either.

@parkerstevenson, could you please confirm/deny if the error appears even after removing the zero variation genes? if so, do the vignette example run fine? What is the version/platform of the CoGAPS you are using?

thanks in advance!

[dimalvovs]

Closing as not enough details to reproduce.