Subtypes from bulk RNA-seq to scRNA-seq
Hi,
I used the NMF method to decompose TCGA RNA-seq data and classified the samples into three subtypes. Now I want to attempt selecting a group of single-cell samples that correspond to these three subtypes to explore the differences among these subtypes from the perspective of scRNA-seq. However, I am not sure how to select single-cell samples that align with the subtypes identified based on bulk RNA-seq data. Could you give me some suggestions?
Thanks
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please give more information about the TCGA RNA-seq which cancer type you did work on so that it would be easy for others to help or suggest
Hi, 1769mkc
Thank you for yuur replying. I focused on the breast cancer in early stage and collected these early stage samples according to the TMN stage. Then, I applied NMF method to the RNA-seq data of these samples. The results indicated that these samples could be divided into three subgroups. Now, I wanted to further investigate the difference between these three subgroups in scRNA-seq data. I am not sure how to classified sepecific sample from the scRNA-seq into these three subgroups. Please give me some suggestions on how to do it.
Thanks