Hello!
I’ve been trying to perform enrichment analysis of my data but keep running into an error - " Error in all.mzsp[i, ] : subscript out of bounds" while trying to perform PSEA. Here’s my R session info for reference:
mSet1 ← PreparePrenormData(mSet1)
mSet1 ← Normalization(mSet1, “NULL”, “LogNorm”, “NULL”, ratio=FALSE)
mSet1 ← PlotNormSummary(mSet1, “norm_newest_”, “png”, 72, width=NA)
mSet1 ← PlotSampleNormSummary(mSet1, “snorm_newest_”, “png”, 72, width=NA)
mSet1 ← SetPeakEnrichMethod(mSet1, “mum”, “v2”)
mSet1 ← PreparePeakTable4PSEA(mSet1)
[1] “Performing regular t-tests …”
[1] “A total of 3936 significant features were found.”
mSet1 ← SetMummichogPval(mSet1, 0.05)
mSet1 ← PerformPSEA(mSet1, “hsa_mfn”, “current”, 3 , 100)
trying URL ‘https://www.metaboanalyst.ca/resources/libs/mummichog/hsa_mfn.qs’
Content type ‘unknown’ length 840638 bytes (820 KB)
downloaded 820 KB
[1] “Got 3936 mass features.”
Error in all.mzsp[i, ] : subscript out of bounds
On checking the file “raw_dataview”, I noticed that the mode was “negative”, though the mode for my dataset is “mixed”, containing both positive and negative. Even when I changed the mode to positive manually, I got the same error.
Please help!