ChemStation batch export help

[gcpat]

Hi,

I'm trying to help my friend with chemstation. She has ChemStation rev A.10. She has a .b batch file with data from 60 runs. She has gone through and manually adjusted some integration baselines and the adjustments are saved & restored the next time she loads the .b file.

She wants to export the data to excel. She can use the menu entry File -> Export -> CSV to export the 'integration results' table, and she gets exactly what she wants. She is interested in the Time & Area fields. The only problem is that it is tedious to do this for all 60 runs.

Is there a way to use macros to automate the process? When the .b file is loaded there is a 'next run' button to click to load the next run, and then we have to click through the export dialog each time. Thanks!

Pat

[Garlarg]

Maybe try this:

http://www.chemuserworld.com/software/chemexcel.zip

Very handy in excel data export.

[lmh]

You don't need macros.

In batch mode, go to Batch - Options (also accessible via a button on the batch bar at the bottom of the screen)

Use the tab Report Table to set up what data you would like to export. It can export peak areas, calculated amounts and retention times for any peak you have set up as a calibrated thing.

Use the tab Report Options to choose the filename and type. You will probably want to export an excel file.

Now use "Batch" - "Output batch report" to create the file. If you look at the excel file it will have three worksheets. The first is useless. The second contains the column names. The third contains the data tabulated for all peaks in all samples.

A note on batch files: the first time you open a batch file, you get an option of opening it with a different method, which is helpful if you have set up a separate data-processing method to your instrument method. If you resave your batch file, you never get this option again! You can still process by a different method, but you have to save your old method by which the batch file was processed with some other name, and save the new method by which you would like to process it in the name it is expecting to see!

Another note: Exit batch review is next to Output batch report in the menus! It is really anoying to exit when you wanted to save the file...

[lmh]

Oh, and the "start" button processes all files in a batch automatically...

[gcpat]

Thank you for this very clear explanation. I have tried Batch Report before, but I do not recall seeing the Report Table tab, so maybe there is an option I missed. I will give it another try.

When I tried the Batch Report feature before, it did indeed write the data to a three sheet excel file, but the exported numbers did not exactly match some of the numbers in the integration results table, such as the manually adjusted baselines.

You say, 'for any peak you have set up as a calibrated thing.' I'm not sure the peaks we're adding using manually placed baselines are part of any calibrations or calibration tables. We are doing our own calibration in excel external to ChemStation after we copy the numbers out of ChemStation. We're really only using ChemStation for manually adjusting integration baselines. If there is some calibration feature I could use that would make batch report work better, that would be great.

[lmh]

OK, I'll put my hands up: I have no idea whether it's possible to use batch export to export manually-adjusted baselines. If you really need to use manual integration, I may have answered the wrong question (sorry!).

But I'd suggest you look into what Chemstation can do: Firstly, it may be that you don't need manual integration. Have you tried the different sorts of baseline that Chemstation offers (advanced, classic, no penetration etc.)? Adjusting these, and choosing good integration parameters might avoid the need for manual alterations (good starting-conditions can be obtained by choosing a weak signal and using autointegrate). Note that you can set individual integration parameters for each signal of interest (or change entire defaults for a detector if you prefer). The exception is the baseline; if you choose "advanced", then everything will be "advanced" (usually no bad thing!).

There was a lengthy debate here a while back on the subject of manual integration, and its acceptability. As I remember, we agreed to differ, but the consensus was manual is OK, but if you can use automatic, it raises less awkward questions about validation, as well as being easier. The old hands reckoned they can do a better job than automatic; us newbies reckoned we like our automatic and if a chromatogram is so bad we can't get it to integrate automatically, it probably isn't worth manual attention anyway! There was a side-debate on smoothing; I personally love well-done smoothing, especially for low-abundance MS data, because integrators do a much better job when not fooled by noise, but others are quite adamant it's totally unacceptable as manipulation of the data.

Secondly, Chemstation does external and internal calibration curves quite nicely (note: you have to choose whether you want internal or external in define report, not in set up calibration!), certainly with more convenience than exporting to Excel. Simply define your signals, define your peaks in the calibration table, and add levels for all your standards. Enter into "amount" the amounts in each standard. The table will be calibrated as you go along if you open each data file for a standard, and use "add level" to add its amount. Minor note: "new calibration table" messes up some signal details (particularly smoothing) which need repairing after starting a new cali table. If you've set up a cali table once, and you are recalibrating, you can open the standard and click on recalibrate, and it will change the corresponding point in the calibration curves. These can all be viewed, exported etc.

Batch processing, assuming you have not defined samples as standards in the sequence, uses the existing calibration curves embedded in the method to calculate all samples. It works differently to running a sequence where standards are defined, in that there is no bracketing: it simply uses the embedded curve for the entire batch, with no changes.

Good luck!

[silhouette]

Maybe try this:

http://www.chemuserworld.com/software/chemexcel.zip

Very handy in excel data export.

Any chance to mail this to me since link is broken ?

my mail : ----

Thanks