GEOMX SPATIAL TRANSCRIPTOMICs

Question

[Nai]

I am naive in geomx transcriptomics data analysis. I have fastq files and few images. How should I follow with this data analysis in bioinformatics pipeline

Answer 1

[GenoMax]

See my answer here: GeoMX NGS RNASeq data analysis

Also: Spatial Transcriptomics : Nanostring GeoMx DSP

[Nai]

Thank you for this. I am struggling in that post regarding GEOMX workflow. I am going through GEOMX workflow with demo data (https://bioconductor.org/packages/devel/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#4_QC__Pre-processing). I have DCC files. Which PKC files has to be selected for any cancer and kidney demo data. If the data is fresh then annotation file is in xlsx format. Now in Demo data what should I use?

1. phenoDataFile = SampleAnnotationFile, (#this is own annotation file)

                      phenoDataSheet = "Template",
                      phenoDataDccColName = "Sample_ID",
                      protocolDataColNames = c("aoi", "roi"),
                      experimentDataColNames = c("panel"))
   

I am not getting this information. If I am getting right, these columns will be selected from annotation file. PhenoDataSheet?