Problem identification Macro

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farid

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Jul 24, 2013, 6:03:54 AM7/24/13
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Hello,

I have a problem during the identification macro of ideom V19. The process stops at 70%.

The debug mode gives me this message :


Else
    With Selection.Validation
        .Delete
        .Add Type:=xlValidateList, AlertStyle:=xlValidAlertWarning, Operator:= _
        xlBetween, Formula1:= _
        "=OFFSET(formulacell,MATCH(C2,DBform,0),1,COUNTIF(DBform,C2),1)"
        .IgnoreBlank = True
        .InCellDropdown = True
        .InputTitle = ""
        .ErrorTitle = "Caution"
        .InputMessage = ""
        .ErrorMessage = "This metabolite name is not in the DB. Please add new metabolites to the DB to access full features."
        .ShowInput = True
        .ShowError = True
    End With



Thank you in advance for your help.

Best regards,

Farid

farid

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Jul 24, 2013, 8:51:39 AM7/24/13
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I saw that vincent bonifay had the same problem "erreur 1004". I tried with the version available on sourceforge.net (Version modified 2013-06-26) with no success. Is it the last version available?

Best regards,

Farid

Darren

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Aug 7, 2013, 2:02:45 AM8/7/13
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Hi Farid, 
Thanks for the report and the extra information provided. It seems that your laptop crashed because it did not have enough memory to process the large dataset. However, the reason the dataset was so large was because the raw data was in profile mode, not centroid mode.

To avoid these issues be sure to use centroided data (i.e. not Profile mode). The CentWave algorithm in XCMS (which the standard IDEOM pipeline uses for high-resolution data) is designed to only work on centroid data. 

If you have collected Raw data in Profile mode then you can easily convert to centroid during the conversion to mzXML format. The IDEOM script for msconvert (step (b) in IDEOM) will automatically centroid the files.  If you are doing it manually in msconvert please select the 'Peak Picking' filter in the GUI, or add this filter to the command line:  --filter \"peakPicking true 1\"

all the best

regards,
Darren

farid

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Aug 25, 2013, 4:52:03 AM8/25/13
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Hi Darren, 

Usually, i record my mass spectrum in profile mode. I will try in centroid mode in order to compare the gap in number of features between the both mode.

Thanks a lot for work, you have a done a nice work. I will wait with interest the future version of ideom.

Cheers,

Farid
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