Input file for your own experiment

DavisLaboratory / standR

Spatial transcriptomics analyses and decoding in R

https://davislaboratory.github.io/standR/

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Input file for your own experiment #30

Closed willros closed 2 months ago

willros commented 4 months ago

Hi!

I have one question regarding the input files needed for running an analysis on data from your own experiment.

How do I generate the files:

countfile: count.txt
sampleAnnoFile: metadata.txt
featureAnnoFile: genemeta.txt ... from my own data?

It would be really helpful if you can say something about this.

Thank you for your work! William

ningbioinfo commented 4 months ago

Hi William,

In my experience with Nanostring GeoMx, they usually give you a couple of excel files that include multiple sheets. The count table and metadata are usually in one of the sheets within the excel files.

willros commented 4 months ago

Thanks for answering, @ningbioinfo.

Ok, so after the .dcc files are uploaded to the geomx machine again? I will try that later.

hookoop commented 3 months ago

Hey, we solved this issue!

You have to upload the DCC files to the GeoMX Data analysis suite, from where you can export an excel that contains several sheets. You first have to save the sheets separately, and then open them in R. The sheets contain information for the sampleAnnoFile, feautureAnnoFile, and countfile so we subsetted them in R.

Best, Helka

ningbioinfo commented 3 months ago

Hi @hookoop , thanks for the answer!

willros commented 3 months ago

Thanks! I found the correct files!