Hi all, new to Bioconductor/scRNA-seq analyses here.
For an upcoming project, I have chosen to analyze this dataset, "Generation of a Broadly Useful Model for COVID-19 Pathogenesis, Vaccination, and Treatment".
I have preprocessed and loaded the .tsv file (from supplemental files in GEO) into a SingleCellExperiment. My understanding is that the row names are the individual mouse genes and the column names are the six samples that were taken.
Here is how my SingleCellExperiment looks in R:
> sc3.sc #what my sce is called class: SingleCellExperiment dim: 55339 6 metadata(0): assays(1): counts rownames(55339): 0610005C13Rik 0610006L08Rik ... n-TStga1 SARS-CoV-2 rowData names(0): colnames(6): Ad5.Empty.rep1 Ad5.Empty.rep2 ... Ad.hACE2.rep2 Ad.hACE2.rep3 colData names(0): reducedDimNames(0): altExpNames(0):
What is your advice going forward/what should my end product be?
Furthermore, can I create a clustering map with this type of data/how applicable will that be with this dataset (individual cells do not seem to be in the columns, as there are only 6)?