Open windtalker6 opened 2 years ago
Thanks for your test on msisensor and msisensor2, and msisensor2 uses ~3000 site models trained from TCGA ~1500 WES samples. We can not gurante 100% AUC for WES tumor only data, so we absolutely recommend using msisensor if tumor-normal paired data in place.
I suppose these two samples sequencing data should be based on some kind of custrom gene panel in which there are only 159 msisensor2 models. So, I think the recommended 10% cutoff is not suitable for this custom gene panel.
Thanks for your test on msisensor and msisensor2, and msisensor2 uses ~3000 site models trained from TCGA ~1500 WES samples. We can not gurante 100% AUC for WES tumor only data, so we absolutely recommend using msisensor if tumor-normal paired data in place.
I suppose these two samples sequencing data should be based on some kind of custrom gene panel in which there are only 159 msisensor2 models. So, I think the recommended 10% cutoff is not suitable for this custom gene panel.
yes, these two samples are sequenced using a panel of ~700 genes.
for msisensor, the 10% cutoff value is ok, which can differentiate MSI-H and MSS. while for msisensor2, the 20% cutoff seemed to be two high for my data
Thanks for your test on msisensor and msisensor2, and msisensor2 uses ~3000 site models trained from TCGA ~1500 WES samples. We can not gurante 100% AUC for WES tumor only data, so we absolutely recommend using msisensor if tumor-normal paired data in place.
I suppose these two samples sequencing data should be based on some kind of custrom gene panel in which there are only 159 msisensor2 models. So, I think the recommended 10% cutoff is not suitable for this custom gene panel.
then can you give me some advice on choosing a new cutoff value for msisensor2 ?
I wonder is there any cut-off threshold for the msisensor2 to difined msi-L
thank you for your attention
I test msisensor and msisensor2 in 2 samples(22SSP1000008 and 22SSP1000009)
both the two sample has tumor bam files and matched normal bam files.
for 22SSP1000008, which is MSI-H when using msisensor(tumor+normal):
which is MSI-H according to https://github.com/ding-lab/msisensor/issues/29 (cutoff: 10%)
msisensor2 result:
which is MSI-L or MSS according to https://github.com/niu-lab/msisensor2/issues/3 (cutoff: 20%)
while for 22SSP1000009, which is MSS
msisensor produced :
msisensor2 output:
exactly the same, both of them are MSS.