centroided NA cannot combine imzML files

[Sandra Murphy]

Hello everyone,

I'm new to MSI and have just started playing around with Cardinal for my data analysis! So far it's great and works really well for my single files.

However, I have multiple imzML files (exported from FlexImaging, data was acquired with a RapifleX) which I would like to combine before doing my pre-processing. However, when I use cbind or combine I get the following error :

Error in if (!all(is_centroided) && !all(!is_centroided)) .warning("all object must be centroided or not centroided") :

missing value where TRUE/FALSE needed

Indeed when I look at my datasets, centroid is NA. Is there something I can do to prevent/fix this, please?

This is the information for one of my datasets:

An object of class 'MSContinuousImagingExperiment'  

<17835 feature, 3578 pixel> imaging dataset   

imageData(1): intensity    

featureData(0):   

pixelData(0):    

metadata(11): ibd binary type universally unique identifier ... files name    

run(1): NHL113_DHAP_2_20kDa    

raster dimensions: 51 x 73    

coord(2): x = 39..89, y = 21..93    

mass range:  2199.459 to 20000.438     

centroided: NA 

Thanks in advance for your help!

Sandra

[kbemis]

You can set this manually if it can't be inferred from the imzML file:

centroided(mydata) <- FALSE

[Sandra Murphy]

That was embarrassingly easy to fix! 

Thank you so much for your quick response and help- my files combine perfectly now.

Looking forward to using the package some more!