Warning: Large values detected, is data log transformed?

[mumdark]

Thank you for developing such an excellent tool.

I am conducting single-cell analysis, and when running the following code:

pdac_epi_result <- CoGAPS(pdac_epi_counts, pdac_params)

I receive the following warning:

Warning: Large values detected, is data log transformed?

Meanwhile, I noticed the following line of code in the vignette, but the generated norm_pdac_epi_counts does not seem to be used:

norm_pdac_epi_counts <- log1p(pdac_epi_counts)

Is there any mistake in my analysis?

Thanks for your help!

[ejfertig]

You should probably use the normalized values as input instead of counts

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From: 酩酊 @.> Sent: Tuesday, July 9, 2024 6:03:02 AM To: FertigLab/CoGAPS @.> Cc: Subscribed @.***> Subject: [FertigLab/CoGAPS] Warning: Large values detected, is data log transformed? (Issue #113)

Thank you for developing such an excellent tool.

I am conducting single-cell analysis, and when running the following code:

pdac_epi_result <- CoGAPS(pdac_epi_counts, pdac_params)

I receive the following warning:

Warning: Large values detected, is data log transformed?

Meanwhile, I noticed the following line of code in the vignette, but the generated norm_pdac_epi_counts does not seem to be used:

norm_pdac_epi_counts <- log1p(pdac_epi_counts)

Is there any mistake in my analysis?

Thanks for your help!

— Reply to this email directly, view it on GitHubhttps://github.com/FertigLab/CoGAPS/issues/113, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AATMMK7T6NTAS7UHRYSJP4TZLOYNNAVCNFSM6AAAAABKSQTI5OVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4TONZTGM4DKNA. You are receiving this because you are subscribed to this thread.Message ID: @.***>