Closed pkrog closed 7 years ago
Indeed, running a workflow with multiple assays completely fails:
Hi, for MTBLS338 I get
2017-01-27T12:37:24.129081966Z Error in read.table(argVc["dataMatrix_in"], check.names = FALSE, header = TRUE, :
2017-01-27T12:37:24.129135409Z no lines available in input
2017-01-27T12:37:24.129147410Z Calls: t -> as.matrix -> read.table
2017-01-27T12:37:24.129151256Z Execution halted
The HTML of the downloader does not contain m_*.*
files,
Metabolights study
Investigation file
Study files:
s_MTBLS338.txt
Assay files:
a_MTBLS338_GCMS_Root_met.txt
a_MTBLS338_Root_metabolite_profiling_mass_spectrometry_targeted.txt
a_MTBLS338_negative_Root_met_ms.txt
a_MTBLS338_positive_Root_met_ms.txt
although MTBLS338 has four of them, see ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS338
[FILE] m_MTBLS338_GCMS_Root_met_v2_maf> Oct 04 15:34 305K [VIEW] [DOWNLOAD]
[FILE] m_MTBLS338_Root_metabolite_prof> Oct 04 15:34 823K [VIEW] [DOWNLOAD]
[FILE] m_MTBLS338_negative_Root_met_ms> Oct 04 15:34 5442K [VIEW] [DOWNLOAD]
[FILE] m_MTBLS338_positive_Root_met_ms> Oct 04 15:34 6635K [VIEW] [DOWNLOAD]
Hi @sneumann ,
I'm currently looking at MTBLS338, and improving my script isatab2w4m
.
For two of the assays (a_MTBLS338_GCMS_Root_met.txt
and a_MTBLS338_Root_metabolite_profiling_mass_spectrometry_targeted.txt
) it works well.
However for the other two, it fails. The reason is that the names in the column MS Assay Name
do not match the column names in the matching m_* file.
In fact the names in column MS Assay Name
of file a_MTBLS338_negative_Root_met_ms.txt
seems to match the column names of the positive file m_MTBLS338_positive_Root_met_ms_v2_maf.tsv
and vice versa.
If I guess correctly, this seems to be a mistake. Do you know how to make it corrected?
Thanks for reporting. We had some discussions over MTBLS338 with mtbls-curators, since intensities were collected from either the positive or negative mode assay into the m* file, depending on what polarity works best for this metabolite. So in fact the MAF column names should reflect the s* sample names, instead of assay names. If instead they match the MS assay names of the opposite polarity, that'd be a mistake.
This feature has been developed. Now tool output selected assay and also all assays in W4M format. It can also output mzData and mzML files as collections.
In case of multiple choices inside the Metabolights study, find a way to let the user choose between them, or output all of them.