Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error with some gaussian regression phenotypes #39

Open
kpruss opened this issue Aug 11, 2022 · 0 comments
Open

Error with some gaussian regression phenotypes #39

kpruss opened this issue Aug 11, 2022 · 0 comments

Comments

@kpruss
Copy link

kpruss commented Aug 11, 2022

Hello, I'm testing Scissor with several continuous dependent variables.

info <- Scissor(bulk_dataset = bulk_counts,
sc_dataset = seur_dataset,
phenotype = phenotype,
alpha = NULL,
cutoff = 0.2,
tag = phenotype,
family = "gaussian",
Save_file = 'info.RData') `

My phenotypes are named numeric vectors as follows, a (successful) example:
A_07_L01_01 A_07_L01_03 A_07_L01_04 B_01_L01_04 B_01_L01_05 B_02_L01_08 B_02_L01_09 B_02_L01_10 C_06_L01_01
13.00 12.00 17.20 12.40 6.57 12.80 8.02 23.50 13.10
C_06_L01_02 C_07_L01_04 C_07_L01_06 B_01_L01_01 B_01_L01_02 B_01_L01_03 B_02_L01_06 B_02_L01_07 C_06_L01_03
13.60 8.29 6.29 14.40 16.00 19.30 8.82 11.20 15.90
A_03_L01_01 A_03_L01_02 A_03_L01_03 A_03_L01_04 A_08_L01_05 A_08_L01_06 A_08_L01_07
15.60 12.50 17.50 26.40 25.40 17.60 30.70

Most of the time, the above Scissor command runs successfully. Occasionally, it does not and I receive the following error:
[1] "||"
[1] "Performing quality-check for the correlations"
[1] "The five-number summary of correlations:"
0% 25% 50% 75% 100%
0.01839713 0.26478574 0.32455696 0.37402355 0.52673473
[1] "|
|"
Error in Scissor(bulk_dataset = bulk_counts, sc_dataset = seur_dataset, :
The length differs between tags and phenotypes. Please check Scissor inputs and selected regression type.

For context, the below phenotype led to an error:
A_07_L01_01 A_07_L01_03 A_07_L01_04 B_01_L01_04 B_01_L01_05 B_02_L01_08 B_02_L01_09 B_02_L01_10 C_06_L01_01
10.20 11.40 10.10 7.02 3.42 6.34 8.67 13.30 4.98
C_06_L01_02 C_07_L01_04 C_07_L01_06 B_01_L01_01 B_01_L01_02 B_01_L01_03 B_02_L01_06 B_02_L01_07 C_06_L01_03
6.05 4.61 5.52 8.41 15.60 13.30 6.44 8.73 7.41
A_03_L01_01 A_03_L01_02 A_03_L01_03 A_03_L01_04 A_08_L01_05 A_08_L01_06 A_08_L01_07
9.02 8.87 14.10 9.90 9.79 10.30 11.90

Thanks for your advice.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant