Hello world!
i used infercnv with HMM_type="i6", it's difficult to distinguish the subtypes of neoplastic cells in tumor. in the results, the subtypes shows there are no significantly high cnv score (addition of copies) between subtypes.
in my oppinion, the reason why we cannot use infered cnv result to distinguish the subtypes of neoplastic cells are the CNA states defined by the authors of infercnv are too rare to do distinguishment. in detail, i guessed that there might be 2-fold CNV in lamc2 in PanIN cells with low frequency, but there might be 10-fold CNV with high frequency comparing with normal cells. but in most softwares (e.g. infercnv, starch, cvam), there only 3 states or 6 states (as figure shows), which might be not enough to distinguish the neoplastic cells
there are some solutions of this kind of problems. Thanks for the help!!!!
Hello world! i used infercnv with HMM_type="i6", it's difficult to distinguish the subtypes of neoplastic cells in tumor. in the results, the subtypes shows there are no significantly high cnv score (addition of copies) between subtypes.
in my oppinion, the reason why we cannot use infered cnv result to distinguish the subtypes of neoplastic cells are the CNA states defined by the authors of infercnv are too rare to do distinguishment. in detail, i guessed that there might be 2-fold CNV in lamc2 in PanIN cells with low frequency, but there might be 10-fold CNV with high frequency comparing with normal cells. but in most softwares (e.g. infercnv, starch, cvam), there only 3 states or 6 states (as figure shows), which might be not enough to distinguish the neoplastic cells
there are some solutions of this kind of problems. Thanks for the help!!!!
Bests, Wenhao