Unknown error happened during data normalization process!

MetaboAnalyst
1

Hello, I got an error message " “Unknown error happened during data normalization process!”
Here’s the exact workflow I followed:

  1. Module Used: Statistical Analysis [one factor]

  2. Data Upload: Selected “Peak intensities” and “Samples in columns (unpaired) ”. Then uploaded my data in a csv file.

  3. Missing value: remove features with ＞ 70％ missing values and replace by LoDs (1/5 of the minimum positive value of each variable). Then clicked Submit → Proceed.

  4. Data Filtering:
    Unchecked reliability filter.
    Checked interquantile range (IQR) and set to 5%.
    Checked mean intensity value at 0%.
    Clicked Proceed.

  5. Normalization:
    Checked “Normalization by sum”.
    Applied log transformation (base 10).
    Data scaling: “None”
    Clicked “Normalize”.

At this point, I received the error:
“Error: Unknown error happened during data normalization process!”
20250702.csv (28.9 KB)

Thank you for help!

2

Thanks for your question. I followed the exact same process, and it worked for me. Could you please confirm if the followings are the exact R commands executed?

1. mSet<-InitDataObjects(“pktable”, “stat”, FALSE, 150)
2. mSet<-Read.TextData(mSet, “Replacing_with_your_file_path”, “colu”, “disc”);
3. mSet<-SanityCheckData(mSet)
4. mSet<-PlotMissingDistr(mSet, “qc_miss_0_”, “png”, 150, width=NA)
5. mSet<-RemoveMissingPercent(mSet, percent=0.7)
6. mSet<-ImputeMissingVar(mSet, method=“lod”, grpLod=F, grpMeasure=F)
7. mSet<-FilterVariable(mSet, “F”, 25, “iqr”, 5, “mean”, 0)
8. mSet<-PreparePrenormData(mSet)
9. mSet<-Normalization(mSet, “SumNorm”, “LogNorm”, “NULL”, ratio=FALSE, ratioNum=20)
10. mSet<-PlotNormSummary(mSet, “norm_0_”, “png”, 150, width=NA)
11. mSet<-PlotSampleNormSummary(mSet, “snorm_0_”, “png”, 150, width=NA)
3

Thank you for your prompt reply. Here’s the exact R commands I followed:
|1.|mSet<-InitDataObjects(“pktable”, “stat”, FALSE, 150)|
|2.|mSet<-Read.TextData(mSet, “Replacing_with_your_file_path”, “colu”, “disc”);|
|3.|mSet<-SanityCheckData(mSet)|
|4.|mSet<-PlotMissingDistr(mSet, “qc_miss_0_”, “png”, 150, width=NA)|
|5.|mSet<-RemoveMissingPercent(mSet, percent=0.7)|
|6.|mSet<-ImputeMissingVar(mSet, method=“lod”, grpLod=F, grpMeasure=F)|
|7.|mSet<-FilterVariable(mSet, “F”, 25, “iqr”, 5, “mean”, 0)|
|8.|mSet<-PreparePrenormData(mSet)|
|9.|mSet<-Normalization(mSet, “SumNorm”, “LogNorm”, “NULL”, ratio=FALSE, ratioNum=20)|.
Then I still got the error message.