TME_deconvolution_all function error

[kestlermai]

library(immunedeconv)

devo <- TME_deconvolution_all(list_train_vali_Data)

--- Data preprocessing --- Error in select(., -c(ID, OS.time, OS)) : unused argument (-c(ID, OS.time, OS))

sessionInfo()

other attached packages: [1] magrittr_2.0.3 immunedeconv_2.1.0 EPIC_1.1.7 forestploter_1.1.1 meta_7.0-0
[6] metadat_1.2-0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 purrr_1.0.2
[11] readr_2.1.5 tidyverse_2.0.0 survivalROC_1.0.3.1 survminer_0.4.9 ggpubr_0.6.0
[16] aplot_0.2.2 risksetROC_1.0.4.1 data.table_1.15.4 mixOmics_6.24.0 lattice_0.22-5
[21] MASS_7.3-60.0.1 ggbreak_0.1.2 tidyr_1.3.1 ggsci_3.0.3 ggplot2_3.5.0
[26] compareC_1.3.2 miscTools_0.6-28 BART_2.9.9 nlme_3.1-164 tibble_3.2.1
[31] dplyr_1.1.4 survivalsvm_0.0.5 CoxBoost_1.5 prodlim_2023.08.28 gbm_2.2.2
[36] superpc_1.12 plsRcox_1.7.7 glmnet_4.1-8 randomForestSRC_3.3.0 survival_3.5-8
[41] Matrix_1.6-5 Mime1_0.0.0.9000

[l-magnificence]

This is not an error of the function. Please check the format of input data.

[kestlermai]

Oh！thanks, it's working.

[weifuq]

[l-magnificence]

Due to that immune microenvironment deconvolution are processed by R package immunedeconv (https://github.com/omnideconv/immunedeconv), you can try to use this package directly and see if it can run successfully and contact them for issue.

[123wanguang123456]

Oh！thanks, it's working.

@kestlermai

Hello, how to solve this error?

--- Data preprocessing --- Error in select(., -c(ID, OS.time, OS)) : unused argument (-c(ID, OS.time, OS))

[kestlermai]

@l-magnificence @123wanguang123456 Hey, After debugging, I found that there’s a conflict between the cal_AUC_ml_res function and the TME_deconvolution_all function. I think it’s due to some package conflicts, maybe the dplyr package. So, you need to restart your R Studio, reload the Mime1 and immunedeconv packages, and then directly run TME_deconvolution_all function. It should work fine then.

[123wanguang123456]

@kestlermai Thank you for your careful answer. I have done so according to what you said, but I still report this error. Is there any good way?

devo <- TME_deconvolution_all(list_train_vali_Data) --- Data preprocessing --- Error in select(., -c(ID, OS.time, OS)) : unused argument (-c(ID, OS.time, OS))

[l-magnificence]

@123wanguang123456 Please reinstall and retry.

[rayrayhuang]

Hello, how to solve this error?

[l-magnificence]

@rayrayhuang Have you reinstalled and retry? We have made some updates.

[rayrayhuang]

@rayrayhuang Have you reinstalled and retry? We have made some updates. I reinstalled the package and still reported this error

[l-magnificence]

@rayrayhuang I'm confused that this shouldn't happen in the latest version. If you still want it, I recommend you do the analysis yourself directly using the R package immunedeconv.