Error when loading my data

[cindy]

Hi,

I tried to load my file using:

d <- readImzML("Slide1-Pten-WT2-neg/Slide1-Pten-WT2-neg")

and I got this error:

reading imzML file: '/Users/txd/Desktop/cardinal3/Slide1-Pten-WT2-neg/Slide1-Pten-WT2-neg.imzML'
detected ibd binary type: ‘continuous’
detected representation: ‘centroid spectrum’
reading ibd file: '/Users/txd/Desktop/cardinal3/Slide1-Pten-WT2-neg/Slide1-Pten-WT2-neg.ibd'
Error in validObject(.Object) :
  invalid class “MSContinuousImagingExperiment” object: number of rows in 'featureData' must match number of rows in 'imageData'

What should I do to read the data?

Thanks!

[Giulia Ricciardi]

Hi Cindy,

to load a file try using the following code:

myFile <- " C:/Users/txd/Desktop/cardinal3/Slide1-Pten-WT2-neg/Slide1-Pten-WT2-neg.imzML " 
d <- readMSIData(myFile)

In the first line, you should specify the path. You may not need the 'C:' at the beginning of the line, but that depends on how your computer wants the path to be written.

Let me know how this works out!

Best,

Giulia

[cindy]

Hello Giulia,

I'm still getting the same error, which I think might not be an issue with the file path, but rather with my data.

> myFile <-"/Users/txd/Desktop/cardinal3/Slide1-Pten-WT2-neg/Slide1-Pten-WT2-neg.imzML"
> d <- readMSIData(myFile)

reading imzML file: '/Users/txd/Desktop/cardinal3/Slide1-Pten-WT2-neg/Slide1-Pten-WT2-neg.imzML'
detected ibd binary type: ‘continuous’
detected representation: ‘centroid spectrum’
reading ibd file: '/Users/txd/Desktop/cardinal3/Slide1-Pten-WT2-neg/Slide1-Pten-WT2-neg.ibd'
Error in validObject(.Object) :
  invalid class “MSContinuousImagingExperiment” object: number of rows in 'featureData' must match number of rows in 'imageData'

[Giulia Ricciardi]

Hello!
I'm not sure about what could be the issue here. Maybe you can try to convert your data from 'continuous' to 'processed'.

myFile_proc <- as(myFile, "MSProcessedImagingExperiment")

myFile_proc