error when running pySCENIC

[aertslab]

error when running pySCENIC

[bramvds]

Are you sure the expression matrix contains only numerical values?

[WRui]

Yes, I am sure the expression matrix contains only numerical valus. The screenshot is the head line of my matrix. [email protected] From: Bram Van de Sande Date: 2018-03-20 17:31 To: aertslab/pySCENIC CC: fish_cat; Author Subject: Re: [aertslab/pySCENIC] error when running pySCENIC (#2) Are you sure the expression matrix contains only numerical values? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[WRui]

hi, I also try the test matrix (GSE60361) but got the same error, too. I wonder whether you have any ideals about it ? Thanks you Best wishes [email protected] From: Bram Van de Sande Date: 2018-03-20 17:31 To: aertslab/pySCENIC CC: fish_cat; Author Subject: Re: [aertslab/pySCENIC] error when running pySCENIC (#2) Are you sure the expression matrix contains only numerical values? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[tmoerman]

Probably this is the problem: "(expression_matrix, gene as rows and samples as columns)"
GRNBoost expects samples as rows and genes as columns.

[WRui]

Thanks for you reply. Actually, I have seted the '-T' parameters when running the pySCENIC and also have tried to convert the matrix first and then runned the pySCENIC but all meet the same error above.