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SingleR: did not converge in 10 iterations #248

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abulislam opened this issue Oct 25, 2023 · 0 comments
Open

SingleR: did not converge in 10 iterations #248

abulislam opened this issue Oct 25, 2023 · 0 comments

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@abulislam
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abulislam commented Oct 25, 2023

How to increase iterations or solve the following problem?

anno <- SingleR(test = ourSCE,
ref = refSCE,
assay.type.test = "logcounts",
assay.type.ref = "logcounts",
labels = refSCE$cellType,
aggr.ref = TRUE)

              > warnings()

Warning messages:
1: did not converge in 10 iterations
2: did not converge in 10 iterations
3: did not converge in 10 iterations
4: did not converge in 10 iterations
5: did not converge in 10 iterations
6: did not converge in 10 iterations
7: did not converge in 10 iterations
8: did not converge in 10 iterations
9: did not converge in 10 iterations
10: did not converge in 10 iterations
11: did not converge in 10 iterations
12: did not converge in 10 iterations
13: did not converge in 10 iterations
14: did not converge in 10 iterations
15: did not converge in 10 iterations
16: did not converge in 10 iterations
17: did not converge in 10 iterations
18: did not converge in 10 iterations
19: did not converge in 10 iterations

Warning messages:
1: Quick-TRANSfer stage steps exceeded maximum (= 17474850)
2: did not converge in 10 iterations
3: Quick-TRANSfer stage steps exceeded maximum (= 20376350)

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