need help analyzing Geomx spatial transcriptomics data

Question

[Cony Lab]

Hello, everyone, I need to analyze Geomx spatial transcriptomics data, and I can get the data from https://nanostring.com/products/geomx-digital-spatial-profiler/spatial-organ-atlas/human-brain/

but when I try to do this:

 # automatically list files in each directory for use
DCCFiles <- dir(file.path(datadir, "dccs"), pattern = ".dcc$",
                full.names = TRUE, recursive = TRUE)
PKCFiles <- unzip(zipfile = dir(file.path(datadir, "pkcs"), pattern = ".zip$",
                                full.names = TRUE, recursive = TRUE))
SampleAnnotationFile <-
    dir(file.path(datadir, "annotation"), pattern = ".xlsx$",
        full.names = TRUE, recursive = TRUE)

We then load the data to create a data object using the readNanoStringGeoMxSet function.

# load data
demoData <-
    readNanoStringGeoMxSet(dccFiles = DCCFiles,
                           pkcFiles = PKCFiles,
                           phenoDataFile = SampleAnnotationFile,
                           phenoDataSheet = "Template",
                           phenoDataDccColName = "Sample_ID",
                           protocolDataColNames = c("aoi", "roi"),
                           experimentDataColNames = c("panel"))

I don't know what should be the annotation files, or do I need to create one? I'm so confused.

Answer 1

[4732b159]

Hello, The annotation file is generated from the DSP machine once you upload the DCC counts which then can be modified depending on the specific annotations/groups etc. you like to use in the analysis pipeline. BW