Seurat: Seurat Version 3 Vlnplot in integrated analysis

[rajasreemenon]

Hi,
I am getting negative values for one dataset when I do integrated analysis of two seurat objects and view the gene expression per cluster using vlnplot. Please see the plot below.
Any suggestion is greatly appreciated.

Thank you,
Raji

[rmenafra]

I think it's related to the active assay you have. If you don't switch that from Integrated to RNA then you see those negative values. You can switch assay by typing DefaultAssay(object.combined) <- "RNA". Hope this helps.
Best,
Roberta

[rajasreemenon]

Thank you Roberta.

Raji

---

From: rmenafra [e-mail]
Sent: Thursday, May 9, 2019 5:10:48 AM
To: satijalab/seurat
Cc: rajasreemenon; Author
Subject: Re: [satijalab/seurat] Seurat Version 3 Vlnplot in integrated analysis (#1514)

External Email - Use Caution

I think it's related to the active assay you have. If you don't switch that from Integrated to RNA then you see those negative values. You can switch assay by typing DefaultAssay(object.combined) <- "RNA". Hope this helps.
Best,
Roberta

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHubhttps://github.com/satijalab/seurat/issues/1514#issuecomment-490823729, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKKY3LUPHAID2HKBFBX5TF3PUPTBRANCNFSM4HLUIPRQ.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[timoast]

We recommend visualizing the uncorrected data, which you can do by switching the assay as pointed out by @rmenafra