merge two SeuratObjects to do the integration

Question

[yueli7]

Hello,

I want to merge two SeuratObjects: h1 and h2, and do the integration.

https://satijalab.org/seurat/pancreas_integration_label_transfer.html

Thank you in advance for great help!

Best,

Yue

> a<-"hc_51_02.csv"
> a1<-data.frame(fread(a),check.names=FALSE, row.names=1)
|--------------------------------------------------|
|==================================================|
> h1<- CreateSeuratObject(counts = a1, project = "h1", min.cells = 3, min.features = 200)
> a<-"hc_52_02.csv"
> a1<-data.frame(fread(a),check.names=FALSE, row.names=1)
> h2<- CreateSeuratObject(counts = a1, project = "h2", min.cells = 3, min.features = 200)

> h1<-readRDS(file="h1.rds")
> h2<-readRDS(file="h2.rds")
> h12<-merge(h1,h2)
Warning message:
In CheckDuplicateCellNames(object.list = objects) :
Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.
> pancreas <- CreateSeuratObject(h12, meta.data = meta.data02)
Error in as.vector(data) : 
no method for coercing this S4 class to a vector
In addition: Warning message:
In CreateSeuratObject(h12, meta.data = meta.data02) :
Some cells in meta.data not present in provided counts matrix.

[GouthamAtla]

What are these h1.rds and h2.rds

[yueli7]

Hello geek_y,

Thank you so much for your response! h1, and h2 are two SeuratObjects.

Thank you again!

Best,

Yue

[GouthamAtla]

If you are merging two seurat objects by merge function from Seurat, the resulting object is a Seurat object. So you dont need to create one. I am not sure what you are trying to do. The link you attached is about data integration and here you are merging.

[yueli7]

Hello geek_y, Thank you so much for your great help! Best, Yue

[2962873004]

The following warning also appeared when I was doing the data merge。What's going on here? How to solve it?

[yueli7]

Hello 2962873004,

Warning is not serious.

Only can create one Seurat object: h1 is already one seurat object, it can not be created twice, so it comes out error.

Best,

Yue

[Bastien Hervé]

I don't really know what you are trying to do writting over on your h1 and h2 variables after creating your seurat objects but you have a merge function in seurat :

pbmc.combined <- MergeSeurat(object1 = pbmc4k, object2 = pbmc8k, add.cell.id1 = "4K", 
add.cell.id2 = "8K", project = "PBMC12K")

https://satijalab.org/seurat/v2.4/merge_vignette.html