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Nesvilab / FragPipeAnalystR

https://www.nesvilab.org/FragPipeAnalystR/
GNU General Public License v3.0
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Phospho_TMT Test data #5

Closed kaupuks closed 2 months ago

kaupuks commented 3 months ago

I tried to repeat the phospho analysis from the data provided. (https://github.com/Nesvilab/FragPipeAnalystR/tree/main/tests/testthat/testdata/3plex_panRCC_TMT)

I got this warning.

plot_pca(se, n=500, ID_col="label") Warning messages: 1: Use of pca_df[[indicate[1]]] is discouraged. ℹ Use .data[[indicate[1]]] instead. 2: Use of pca_df[[indicate[2]]] is discouraged. ℹ Use .data[[indicate[2]]] instead.

Got an error.

prepare_PTMSEA(de_result_updated, "Tumor_vs_NAT_diff", "./result.gct") Error in [.data.frame(as.data.frame(rowData(se)), "SequenceWindow") : undefined columns selected

prepare_kinome(de_result_updated, "Tumor_vs_NAT_diff", "./result.gct") Error in [.data.frame(as.data.frame(rowData(se)), "SequenceWindow") : undefined columns selected

hsiaoyi0504 commented 3 months ago

@kaupuks That's not a phospho data. Instead, it's a global proteome data.