infercnv heatmap appearance of 'Reference' (non-malignant) cells: opinion required

[jjacob12]

Hi, we performed scRNA-seq on human iPSC-derived brain organoids in co-culture with tumour cell-line derived malignant brain cells. The latter cells were not clonal. I performed infercnv analysis using the standard workflow and obtained the attached heatmap

There are equal numbers of cells in the 'References' (non-malignant) as there are in 'Observations' (malignant cells). There is a very obvious difference between the infercnv heatmap profiles, as expected. There are also cells in the 'References' with a weak infercnv signal. I have two alternative explanations for this: 1. could be noise(?) because we recently tested over 600,000 genomic sites of the iPSC line using a SNP array and could not detect any gross chromosomal amplifications, deletions, or re-arrangements. Moreover, iPSC-derived organoids were maintained in culture for only 60 days and were largely maintained in differentiation medium over that time. 2. Organoids contained multiple distinct cell types undergoing differentiation and differentiated cells. The expectation would be that the latter cells would express or repress specific sets of genes that define their identity, so I wonder if it is perhaps not that surprising to see some 'weak' CNV signals in the 'References' cells?