Seurat: Error in creating Seurat Object

[iakovrudenko]

Hi,

I am new to R and Seurat and currently trying to go over tutorial: https://satijalab.org/seurat/immune_alignment.html

I would greatly appreciate if someone can help me to solve simple error.

ctrl <- CreateSeuratObject(raw.data = ctrl.data, project = "IMMUNE_CTRL", min.cells = 5)
Error in CreateSeuratObject(raw.data = ctrl.data, project = "IMMUNE_CTRL", :
unused argument (raw.data = ctrl.data)

Thanks

[Dragonmasterx87]

I think this tutorial is for Seurat v3, and if you did:

Install.packages('Seurat')

You installed v2.3.4 by default.

Have you done the first tutorial? I suggest doing that first, before installing v3.0

I am learning myself, so take what I say with a pinch of salt till a dev comments 👍

[timoast]

If you're learning to use Seurat now I highly recommend installing version 3, going through the v3 tutorials and ignore the v2 tutorials completely. We have a v3 version of the pbmc 3k vignette here: https://satijalab.org/seurat/pbmc3k_tutorial_v3.html

@iakovrudenko, it looks like you have v3 installed but are following the v2 tutorial for immune alignment, you can look at the integration vignette for v3 here: https://satijalab.org/seurat/pancreas_integration_label_transfer.html

[iakovrudenko]

I think this tutorial is for Seurat v3, and if you did:
Install.packages('Seurat')
You installed v2.3.4 by default.
Have you done the first tutorial? I suggest doing that first, before installing v3.0
I am learning myself, so take what I say with a pinch of salt till a dev comments 👍

Thanks, this actually helped.

[iakovrudenko]

If you're learning to use Seurat now I highly recommend installing version 3, going through the v3 tutorials and ignore the v2 tutorials completely. We have a v3 version of the pbmc 3k vignette here: https://satijalab.org/seurat/pbmc3k_tutorial_v3.html
@iakovrudenko, it looks like you have v3 installed but are following the v2 tutorial for immune alignment, you can look at the integration vignette for v3 here: https://satijalab.org/seurat/pancreas_integration_label_transfer.html

Thanks, will try

[Dragonmasterx87]

BTW @timoast nice review in NatRevGenet. Cheers. 🐉