Integrate several CITE-seq data to work on them

[TiphaineCMartin]

Hi,

I would like to integrate several CITE-seq data to be able to identify cells with specific sets of markers and compare between different groups of cells and also between different time point.

I thought to use how you did in https://satijalab.org/seurat/archive/v3.1/immune_alignment.html

`# select features that are repeatedly variable across datasets for integration
features <- SelectIntegrationFeatures(object.list = ifnb.list)

##Perform integration
immune.anchors <- FindIntegrationAnchors(object.list = ifnb.list, anchor.features = features)

this command creates an 'integrated' data assay (bug)

immune.combined <- IntegrateData(anchorset = immune.anchors)`

So I did first
`ifnb.list <- list("day0_none"=seurat_object_day0,
"day1_ctrl"=seurat_object_day1_ctrl,
"day2_vpa"=seurat_object_day2_vpa)

normalize and identify variable features for each dataset independently

ifnb.list <- lapply(X = ifnb.list, FUN = function(x) {
x <- NormalizeData(x)
x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000)
})

select features that are repeatedly variable across datasets for integration

features <- SelectIntegrationFeatures(object.list = ifnb.list)`

but when I run immune.combined <- IntegrateData(anchorset = immune.anchors)
I have this error message

Merging dataset 2 into 1
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 1 2 into 3
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
Error in idx[i, ] <- res[[i]][[1]] :
number of items to replace is not a multiple of replacement length
In addition: Warning message:
In RunIntegration(filtered.anchors = filtered.anchors, normalization.method = normalization.method, :
Number of anchors is less than k.weight. Lowering k.weight for sample pair.

Do you know what I need to look at to solve this issue?
Do I need to use another method to integrate CITE-seq data?

Thanks,
Tiphaine