Seurat: how to create seurat object using GEO data?

[YidingZhang117]

I'm wondering about how to use the single cell data provided in GEO. It provides SOFT formatted family file(s), MINiML formatted family file(s) and Series Matrix File(s). Which one do I need to use? I think they are raw data right? Should I use CreateSeuratObject function to transform the data in GEO to seurat object or some other R package is needed? Thank you very much if you can help me on this!

[mojaveazure]

CreateSeuratObject takes an expression matrix (sparse or dense) where the columns are cells/samples and the rows are features/genes. While we don't have a function for reading directly from GEO, as long as you can get an expression matrix for the data you're interested in and read it into R (see readMM, read.table, or other functions for reading data into R), you can pass that to CreateSeuratObject

[Diozao666]

I successfully loaded the expression and cell labels in a Seurat object, but even after following the tutorial I don't understand how you can add the metadata using SOFT or xml files, as mentioned by Zhang. The structure of these files don't resemble any other identities tables I have seem in other Seurat objects