Dear colleagues,
we have trained PREFACE on a set of 496 NIPT samples (250 male fœtuses, 246 female fœtuses based on Yfrac) using the following FFY estimation:
FFY = 2 * median bin reads chrY / median bin reads autosomes
Our ${sample}_infile.bed files were prepared from the ${sample}_bins.bed issued by WiseCondorX predict. The training seemed to converge, but performance isn't as good as expected:
We then ran the trained PREFACE model on an independent set of 119 NIPT samples (56 male fœtuses, 63 female fœtuses based on Yfrac), but our Pearson correlation for male fœtuses between FFY and PREFACE_FF is only of 0.64:
We are trying to understand how to improve PREFACE's training. Would you have any recommendations for the training set size? Is there a specific FFY estimation formula that you recommend over the one we used?
Dear colleagues,
we have trained PREFACE on a set of 496 NIPT samples (250 male fœtuses, 246 female fœtuses based on
Yfrac) using the following FFY estimation:FFY = 2 * median bin reads chrY / median bin reads autosomesOur
${sample}_infile.bedfiles were prepared from the${sample}_bins.bedissued byWiseCondorX predict. The training seemed to converge, but performance isn't as good as expected:We then ran the trained PREFACE model on an independent set of 119 NIPT samples (56 male fœtuses, 63 female fœtuses based on
Yfrac), but our Pearson correlation for male fœtuses between FFY and PREFACE_FF is only of 0.64:We are trying to understand how to improve PREFACE's training. Would you have any recommendations for the training set size? Is there a specific FFY estimation formula that you recommend over the one we used?