fineTuningRound method

[xiebb123456]

Hi,

code in fineTuningRound method:

ref_data.filtered = ref_data.filtered[genes.filtered,]
sc_data.filtered = as.matrix(sc_data[genes.filtered])
if (length(genes.filtered)<20) {
return (topLabels[1])
}
if (sd(sc_data.filtered)>0) {
r=cor.stable(sc_data.filtered,ref_data.filtered,method='spearman')
agg_scores = quantileMatrix(r,types.filtered,quantile.use)[1,];
agg_scores = sort(agg_scores,decreasing = T)
agg_scores = agg_scores[-length(agg_scores)]
topLabels = names(agg_scores)[agg_scores>=agg_scores[1]-fine.tune.thres]
}

sc_data.filtered = as.matrix(sc_data[genes.filtered]) missed a ',' , which should be
sc_data.filtered = as.matrix(sc_data[genes.filtered, ])
,so actually the second round with top labels was not run.

what's more, agg_scores = quantileMatrix(r,types.filtered,quantile.use)[1,] didn't get the right cell that needs to 'FineTune ', here recalculate the correlation of sc_data.filtered and ref_data.filtered which could be time cosuming, just need to pick up the cell in sc_data.filtered to do the correlation

Bing

[dviraran]

Hi,

Sorry for the late response. Missed this issue. Anyway, this repository is not supported any more. Please use https://github.com/LTLA/SingleR to report issues.

Best,
Dvir