Cardinal not reading file

[Bailey Polimer]

Hi, 

I have been trying to import msi reader data in the form of an .hdr file into R however I keep receiving the error message "Error: expected file /Users/baileypolimer/Downloads/mse.t2m does not exist". The file exists as an hdr file however the readMSIData function interprets the file as a .t2m file. My code is illustrated as follows. 

library(Cardinal)

readMSIData("/Users/baileypolimerDownloads/mse.hdr")

I have verified that the file exists on the computer at this path however am unsure as to how to follow up with this. 

Thanks, 

Bailey 

[Giulia Ricciardi]

Hi,

in the code you wrote here there is a "/" missing before the word 'Downloads':

readMSIData("/Users/baileypolimerDownloads/mse.hdr")

Please check if it is written correctly in your R console as this may be the reason why you get the error message.

Best,

Giulia

[Bailey Polimer]

I have tried that however I am still getting the error message. The file exists on my computer as a .hdr file however the error says .t2m does not exist. 

[educh...@gmail.com]

Hi, 

Did you try to load readMSIData("/Users/baileypolimerDownloads/mse.img")?

When you load Analyze7.5 format the .img file is the file that “calls” .hdr and .t2m
Best,

Edu

[Giulia Ricciardi]

Hi!

Maybe I've found something!

https://rdrr.io/bioc/Cardinal/man/readMSIData.html

Try using "readAnalyze" instead of "readMSIData"

Hope this helps!

Giulia

[Melanie Föll]

Hi Bailey,

in case you only have an .hdr file, this is not compatible with Cardinal. Cardinal is able to read the Analyze7.5 file format, which consists of three subfiles: hdr + t2m + img. All three files have to have the same name and be located in the same folder. Then you can read them with Cardinal using either readAnalyze("mse") or readMSIData("mse.hdr").

Best,

melanie

[Bailey Polimer]

Oh ok that worked! Thank you so much!