search

bioinfoDZ / RISC

A R package for integrated scRNA-seq data analysis using the RPCI algorithm
Other
42 stars 7 forks source link

Use RISC on a big data #2

Open Zhaohui-Ruan opened 3 years ago

Zhaohui-Ruan commented 3 years ago

Hi, Thanks for making RISC. I am using RISC on big data with 270,000 cells. I got an error as follows when I using RISC on my data. It's seems my data is too large for RISC. Can I just use variable genes matrix to integrate my scRNAseq? Best wish! zhaohui Ruan

image

bioinfoDZ commented 3 years ago

Thanks for your question. We cannot just use variable genes as input to do the integration, because our method will also align gene expression values across data sets. I am not sure what your PC's memory size, usually 1TB should be enough, I tried around 200,000 in our HPC before, with 750GB memory. If your PC does not have enough memory, you could use high threshold to filter the data and reserve the valid cells with extremely good quality. Thanks