Error in approx(lambda, seq(lambda), sfrac) : need at least two non-NA values to interpolate

[baoyulinn]

After i transformed this count into TPM, i use SAVER aging in the same pipelines.
However, i get this error and I want to know the reason. Thank you so much.

> cortex.saver <- saver(tpm, ncores = 12) 18530 genes, 35467 cells starting worker pid=1772768 on localhost:11093 at 12:26:14.811 starting worker pid=1772782 on localhost:11093 at 12:26:15.116 starting worker pid=1772796 on localhost:11093 at 12:26:15.403 starting worker pid=1772810 on localhost:11093 at 12:26:15.691 starting worker pid=1772824 on localhost:11093 at 12:26:15.982 starting worker pid=1772838 on localhost:11093 at 12:26:16.275 starting worker pid=1772852 on localhost:11093 at 12:26:16.561 starting worker pid=1772866 on localhost:11093 at 12:26:16.853 starting worker pid=1772880 on localhost:11093 at 12:26:17.165 starting worker pid=1772894 on localhost:11093 at 12:26:17.459 starting worker pid=1772908 on localhost:11093 at 12:26:17.754 starting worker pid=1772922 on localhost:11093 at 12:26:18.047 Running SAVER with 12 worker(s) Calculating predictions for 15644 genes using 12340 genes and 35467 cells... Start time: 2023-01-13 12:28:11 Estimating finish time... Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Loading required package: SAVER loaded SAVER and set parent environment Finished 12/18530 genes. Approximate finish time: 2023-01-13 12:46:42 Calculating max cor cutoff... loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment Finished 100/18530 genes. Approximate finish time: 2023-01-13 14:16:42 Calculating lambda coefficients... loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment Finished 214/18530 genes. Approximate finish time: 2023-01-13 15:45:52 Predicting remaining genes... loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment loaded SAVER and set parent environment Error in approx(lambda, seq(lambda), sfrac) : need at least two non-NA values to interpolate

`> dim(tpm)
[1] 18530 35467

sum(is.na(tpm))
[1] 0`

[mohuangx]

Can you check if all values in tpm are numeric and non-negative and there are no columns or rows with all zeros?