Hello, I got an error message " “Unknown error happened during data normalization process!”
Here’s the exact workflow I followed:
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Module Used: Statistical Analysis [one factor]
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Data Upload: Selected “Peak intensities” and “Samples in columns (unpaired) ”. Then uploaded my data in a csv file.
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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.
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Data Filtering:
Unchecked reliability filter.
Checked interquantile range (IQR) and set to 5%.
Checked mean intensity value at 0%.
Clicked Proceed.
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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!
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) |
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.