xcms.group error about tools-metabolomics

[lecorguille]

@bernt-matthias
Can you report here (or in Gitter) the lines you got into the stdout of xcms.xcmsSet Merger under XSET OBJECT INFO?

It can be related to this issue: #57

[bernt-matthias]

Here is the output of the (successful) merger step that precedes that failed group step:

	XSET MERGING...
Blanc04 
Blanc06 
Blanc09 
Blanc12 
Blanc15 
Blanc17 
HU_neg_017 
HU_neg_028 
HU_neg_034 
HU_neg_051 
HU_neg_060 
HU_neg_078 
HU_neg_091 
HU_neg_093 
HU_neg_099 
HU_neg_110 
HU_neg_130 
HU_neg_134 
HU_neg_138 
HU_neg_149 
HU_neg_152 
HU_neg_175 
HU_neg_178 
HU_neg_185 
HU_neg_204 
HU_neg_208 
QC1_001 
QC1_002 
QC1_003 
QC1_005 
QC1_006 
QC1_008 
QC1_009 
QC1_011 
QC1_012 
QC1_014 
	XSET PHENODATA SETTING...
	XSET OBJECT INFO
            class
Blanc04     blank
Blanc06     blank
Blanc09     blank
Blanc12     blank
Blanc15     blank
Blanc17      <NA>
HU_neg_017 sample
HU_neg_028 sample
HU_neg_034 sample
HU_neg_051 sample
HU_neg_060 sample
HU_neg_078 sample
HU_neg_091 sample
HU_neg_093 sample
HU_neg_099 sample
HU_neg_110 sample
HU_neg_130 sample
HU_neg_134 sample
HU_neg_138 sample
HU_neg_149 sample
HU_neg_152 sample
HU_neg_175 sample
HU_neg_178 sample
HU_neg_185 sample
HU_neg_204 sample
HU_neg_208 sample
QC1_001      pool
QC1_002      pool
QC1_003      pool
QC1_005      pool
QC1_006      pool
QC1_008      pool
QC1_009      pool
QC1_011      pool
QC1_012      pool
QC1_014      pool
An "xcmsSet" object with 36 samples

Time range: 0.7-1139.5 seconds (0-19 minutes)
Mass range: 50.0606-999.937 m/z
Peaks: 73327 (about 2037 per sample)
Peak Groups: 0 
Sample classes: blank, sample, pool 

Peak picking was performed on MS1.
Profile settings: method = bin
                  step = 0.1

Memory usage: 8.31 MB
	SAVE RData

[bernt-matthias]

Blanc17 <NA> seems fishy .. might this be the problem?

[lecorguille]

I think so! Perhaps a mispelling? Or a sample that is not describe in the sampleMetadata? Le jeu. 25 janv. 2018 à 16:47, M Bernt <[email protected]> a écrit :

…

Blanc17 <NA> seems fishy .. might this be the problem? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#73 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKjyFqTeIE1geRW1ZrxFxWWA5Sz_Hy-Iks5tOKIVgaJpZM4RkfVG> .

[bernt-matthias]

We will check if adding the metadata (which was actually missing from the metadata table) fixes the problem. I will report here.

Nevertheless it might be a good idea to present some prominent warning / error in the merging or grouping step.

[lecorguille]

Sure, I put this #57 on the top of my list :)

[lecorguille]

See #57