# Importing the data set

The original experiment is listed on the Gene Expression Omnibus as GSE848; however, this tutorial only uses a subset of the original experiment and should be downloaded from the Partek website tutorial page, [Gene Expression Analysis with Batch Effects](http://s3.amazonaws.com/partekmedia/tutorials/microarray/Breast-Cancer-GE.zip).

* Download the zipped project folder, *Breast\_Cancer-GE.zip*
* Unzip the project folder to *C:/Partek Training Data/* or a directory of your choosing

This location should be easily accessible. The unzipped *Breast\_Cancer-GE* project folder and a zipped annotation file will be added to the selected directory.

* Unzip the included annotation file, *HG\_U95Av2.na32.annot.rar*
* Move the annotation file, *HG\_U95Av2.na32.annot*, to the microarray libraries folder

By default, the microarray libraries folder will be located at *C:/Microarray Libraries*, but the location may vary depending on your operating system and configuration.

* Open Partek Genomics Suite
* Select (![](/files/l4UTepKJue3s3d3LiYPB)) from the main command bar
* Navigate to the tutorial folder, *Breast\_Cancer-GE*
* Select *Breast\_Cancer.txt*
* Select **Open** (Figure 1)

![](/files/U2DAcuc75klY7ulf8gLU)

Figure 1. Opening a data file. The red Partek Genomics Suite icon is shown next to the data file (FMT file format)

The spreadsheet will open as *1 (Breast\_Cancer.txt)* (Figure 2).

![](/files/zeN4hhqtyG78dYGQlalg)

Figure 2. Breast\_Cancer.txt data file

The summary at the bottom the spreadsheet shows there are 18 rows and 12,631 columns in the spreadsheet. The first column contains the *Filename* listing the GEO GSM number. This is also is an identifier for the microarray. *Treatment*, *Time*, and *Batch* are in columns 2, 3, and 4, respectively. Column 6 marks the beginning of the probesets. The data is log2 transformed.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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