I encountered the following error when running calculate_dif

Calculate difference - label shuffling error about splicingfactory HOT 1 OPEN

esebesty commented on July 19, 2024

Calculate difference - label shuffling error

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Comments (1)

dBenedek commented on July 19, 2024

I also get the error message for a row with 2 unique values and some additional 0s and NAs:

> diversity_data_filtered[404,]

                    ID dataset3_SRX4143134 dataset3_SRX4143118 dataset3_SRX4143107 dataset3_SRX4143157
404 ENSG00000030304.14                  NA          0.03355015                  NA                  NA
    dataset3_SRX4143185 dataset3_SRX4143142 dataset3_SRX4143119 dataset3_SRX4143193 dataset3_SRX4143122
404                   0                   0                   0                  NA            0.999901
    dataset3_SRX4143121
404                   0

difference <- calculate_difference(diversity_data_filtered[404:405,], # 404 - problematic row
                                   samples_data,
                                   control = "control",
                                   method = "mean",
                                   test = "shuffle")

# --> Error in if (ecdf(shuffled[i, ])(log2_fc[i]) >= 0.5) { : 
#  missing value where TRUE/FALSE needed

I guess the reason for this is that the sample number (columns) is low (10), and there are only 2 non-zero/non-NA values, so there will be some problematic groups during the shuffling procedure.

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