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Error when running getActivity_individual() #54

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karlie002 opened this issue Sep 29, 2024 · 2 comments
Open

Error when running getActivity_individual() #54

karlie002 opened this issue Sep 29, 2024 · 2 comments

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@karlie002
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karlie002 commented Sep 29, 2024

Hi ,I'm new to SJARACNe , aftering using downsample to run SJARACNe ,I get consensus_network_ncol_.txt files seperately in TF/SIG,I decided to calculate driver activities with getActivity_individual() , however some error appeared.

截屏2024-09-29 14 53 53

But I have checked that sampleNames of assayData and phenoData are the same and validObject()returns TRUE.

截屏2024-09-29 14 57 19

my code is :
generateSJARACNeInput(input_eset = day7_log2cpm.eset, group_name = "leiden",sjaracne_dir = "./my_path/SJARACNe",species_type = "mm", driver_type = "TF_SIG", downSample_N = 1000)

sjaracne local -e /my_path/day7_Network/SJARACNe/cluster0/cluster0.8154_1000.exp.txt -g /my_path/day7_Network/SJARACNe/cluster0/TF/cluster0.730_1000.tf.txt -o /my_path/day7_Network/SJARACNe/cluster0/TF -n 100 -pc 1e-2 -pb 1e-5 -tmp ./tmp/

activity_cluster0.eset <- getActivity_individual(input_eset = cluster0_day7_log2cpm.eset,network_file.tf = "./SJARACNe/cluster0/TF/consensus_network_ncol_.txt",network_file.sig = "./SJARACNe/cluster0/SIG/consensus_network_ncol_.txt",driver_type = "TF_SIG")

Does anyone have ideas about the source of the error ? Thanks a lot !!

@QingfeiPan
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Hi ,I'm new to SJARACNe , aftering using downsample to run SJARACNe ,I get consensus_network_ncol_.txt files seperately in TF/SIG,I decided to calculate driver activities with getActivity_individual() , however some error appeared.

截屏2024-09-29 14 53 53

But I have checked that sampleNames of assayData and phenoData are the same and validObject()returns TRUE.

截屏2024-09-29 14 57 19

my code is : generateSJARACNeInput(input_eset = day7_log2cpm.eset, group_name = "leiden",sjaracne_dir = "./my_path/SJARACNe",species_type = "mm", driver_type = "TF_SIG", downSample_N = 1000)

sjaracne local -e /my_path/day7_Network/SJARACNe/cluster0/cluster0.8154_1000.exp.txt -g /my_path/day7_Network/SJARACNe/cluster0/TF/cluster0.730_1000.tf.txt -o /my_path/day7_Network/SJARACNe/cluster0/TF -n 100 -pc 1e-2 -pb 1e-5 -tmp ./tmp/

activity_cluster0.eset <- getActivity_individual(input_eset = cluster0_day7_log2cpm.eset,network_file.tf = "./SJARACNe/cluster0/TF/consensus_network_ncol_.txt",network_file.sig = "./SJARACNe/cluster0/SIG/consensus_network_ncol_.txt",driver_type = "TF_SIG")

Does anyone have ideas about the source of the error? Thanks a lot !!

Hi @karlie002 ,

Thanks for your feedback!

We met this error once before, and the reason turned out to be that some symbols in the column names, "-" in that case, were automatically converted to dot (".") during the activity calculation, since by default R doesn't accept "-" in the column names of the data frame. Now we have fixed this error. Would you please reinstall the scMINER R package and try the function getActivity_individual() again?

Best,
Qingfei

@karlie002
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Hi ,I'm new to SJARACNe , aftering using downsample to run SJARACNe ,I get consensus_network_ncol_.txt files seperately in TF/SIG,I decided to calculate driver activities with getActivity_individual() , however some error appeared.
截屏2024-09-29 14 53 53
But I have checked that sampleNames of assayData and phenoData are the same and validObject()returns TRUE.
截屏2024-09-29 14 57 19
my code is : generateSJARACNeInput(input_eset = day7_log2cpm.eset, group_name = "leiden",sjaracne_dir = "./my_path/SJARACNe",species_type = "mm", driver_type = "TF_SIG", downSample_N = 1000)
sjaracne local -e /my_path/day7_Network/SJARACNe/cluster0/cluster0.8154_1000.exp.txt -g /my_path/day7_Network/SJARACNe/cluster0/TF/cluster0.730_1000.tf.txt -o /my_path/day7_Network/SJARACNe/cluster0/TF -n 100 -pc 1e-2 -pb 1e-5 -tmp ./tmp/
activity_cluster0.eset <- getActivity_individual(input_eset = cluster0_day7_log2cpm.eset,network_file.tf = "./SJARACNe/cluster0/TF/consensus_network_ncol_.txt",network_file.sig = "./SJARACNe/cluster0/SIG/consensus_network_ncol_.txt",driver_type = "TF_SIG")
Does anyone have ideas about the source of the error? Thanks a lot !!

Hi @karlie002 ,

Thanks for your feedback!

We met this error once before, and the reason turned out to be that some symbols in the column names, "-" in that case, were automatically converted to dot (".") during the activity calculation, since by default R doesn't accept "-" in the column names of the data frame. Now we have fixed this error. Would you please reinstall the scMINER R package and try the function getActivity_individual() again?

Best, Qingfei

Thank you so much for your quick reply ! I will try to reinstall the R package as you suggested.

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