Fetch public data at GEO and analyse it with IPA (GSE72005)

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Technical.png This page was used to generate data for IPA, for a more complete overview of GEO and public microarray data analysis, please refer to our training pages (http://wiki.bits.vib.be/index.php/Hands-on_Analysis_of_public_microarray_datasets)[1]


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Microarray chip used


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Handicon.png this last info is necessary when uploading in IPA

Quick differential analysis of the GEO dataset GSE72005


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  • define groups based on annotations


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  • control that the signal distribution after normalisation is equivalent for all samples (if very different, abort here!!)


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  • control which statistical choices have been made


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  • start data analysis (takes about one minute)


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  • save full table to your local disk


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  • when the obtained data looks OK, save it to a text file from your browser


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  • take a look (and copy) the R-code that you can use as a starter to go further in RStudio (see tutorial linked above)


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  • re-open the text file in excel (using 'file' 'open') and perform data check as shown below to ensure integrity


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  • save the excel file and use it in IPA


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  • launch IPA, login and create a new project to store your data


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  • upload the excel file


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  • set the context and background according to what the data is then identify all columns you will need in IPA (ID, logFC, and p-values)


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  • play with stringency to obtain less tan 600 genes retained and a nice specificity


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  • for each saved dataset, run a separate core analysis


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you are now ready to play with IPA


download exercise files

Download exercise files here.

Use the right application to open the files present in GSE72005-files

References:
  1. http://wiki.bits.vib.be/index.php/Hands-on_Analysis_of_public_microarray_datasets
  2. http://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE72005



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