Using Seurat to take in a Normalised TPM Gene to Cell matrix as a Seurat Object
Hello everyone, I am trying to import a dataset into RStudio via Seurat as here: www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75688
(filename : GSE75688_GEO_processed_Breast_Cancer_raw_TPM_matrix.txt.g)
This matrix contains normalized tpm values (not log transformed and nor any other processing has been done on it).
What's the recommended way to import the txt matrix file into Rstudio and a Seurat Object(I tried the conversion to csv method via Excel and then easily imported it but was thinking that there could be something easier)?.
Next, I was wondering what's the most efficient route(on the matrix) to apply log transform, further filtration on it(like remove those genes(rows)/cells(columns) with insufficient TPM values or expressive ability across cells), select the HVG genes and eventually perform dimensional reduction and PCA/Cluster analysis. Any commands I need to keep mind of?
Are there any useful threads or tutorials regarding importing and using TPM files directly into Seurat as in the case above as well?
• 39 views