Hey,
I check the FindVariableFeatures() for layers and list+SelectIntegrationFeatures(), the results are same.
The method should be the same one.

Thanks!

HI @Aaron-sqw,
When we find variable features with an object with 2 layers for example, we identify each layer's variable features, find the common variable features, and then supplement until n variable features are present in a list using the most variable features in the two lists that are also features in the other matrices. This is the same as the method we use for identifying features for integration.

To your second question, we don't currently support grouping by multiple variables for integration. However, you can create a variable that contains both tech and sample by pasting the values together and then using this variable for integration. Something like: obj$tech_sample <- paste0(obj$tech, "_", obj$sample). Then you can supply tech_sample for integration.

To your second question, we don't currently support grouping by multiple variables for integration. However, you can create a variable that contains both tech and sample by pasting the values together and then using this variable for integration. Something like: obj$tech_sample <- paste0(obj$tech, "_", obj$sample). Then you can supply tech_sample for integration.

Dear @Gesmira ,
Thanks a lot for your reply!
For the second question, if I set as your method, after split layers, as samples is the smallest element in my project, so paste together should be the same as samples. I tried using the old method RunHarmony(group.by.vars =c("sample","tech")), It seems work that could adjust the batch from two parts.
Whether the new version Seurat V5 could add this group.by.vars parameter in the HarmonyIntegration.

Best,
Aaron

Hi,

Following up on the previous questions, I would like to know can I specify which variables to use for Harmony when using
merge <- IntegrateLayers(
object = merge, method = HarmonyIntegration,
orig.reduction = "pca", new.reduction = "harmony",normalization.method = "SCT",
verbose = FALSE
)
You mentioned @Gesmira in the previous example : "to supply tech_sample for integration" but where do you define it in IntegrateLayers? and which one does it use by default?

Thanks a lot,
Marie

Hi,

Following up on the previous questions, I would like to know can I specify which variables to use for Harmony when using merge <- IntegrateLayers( object = merge, method = HarmonyIntegration, orig.reduction = "pca", new.reduction = "harmony",normalization.method = "SCT", verbose = FALSE ) You mentioned @Gesmira in the previous example : "to supply tech_sample for integration" but where do you define it in IntegrateLayers? and which one does it use by default?

Thanks a lot, Marie

I think you will have to split by that group (e.g. split(obj[["RNA"]], f = obj$tech_sample))