...

The most efficient way of importing array data would be to import them directly from your Partek Flow server. When you select this option, navigate to the folder containing your data files. Valid file types will be selectable for upload. Click on the files you would like to import into the project and select the Create sample button (Figure 1).

 

 

Numbered figure captions
Prefix Figure SubtitleText Importing microarray files into Partek Flow AnchorName Create Samples From Filesimport microarray

During the upload process, Partek Flow will determine the specific platform of your dataset. If they are commonly used chips, such as Affymetrix HTA arrays, the gene and transcript annotations associated with the platform will automatically be downloaded in the Library File Manager.

Once the samples have been uploaded, the Data tab will list each sample along with the Platform associated with each sample. If Affymetrix .CEL files were uploaded, it will also include the date that the array was scanned (Figure 2). This information may be helpful in assessing possible batch effects.

 

Numbered figure captions

...

SubtitleText Imported microarrays will automatically include Platform and, in some cases, Scan date in the Attributes page AnchorName Microarray

...

data tab

Image Modified

You can now add additional sample attributes to your microarray project. For more information on how to set up your project, please refer to the documentation on Creating a project.

...

Once the microarray data has been uploaded, the Microarray intensity data node will appear in the Analyses tab. To convert this data to aligned reads, select the Microarray intensity data node and select the aligner you would like to use for conversion (Figure 3).

 

 

Numbered figure captions
Prefix Figure SubtitleText Converting Microarray intensity to Aligned reads AnchorName Microarray Data Node

 

Selecting an aligner will bring up the Microarray Conversion options page (Figure 4). Under the Select probe sequence file section, make sure that the correct Chip name is specified. For non-custom arrays, these should be set automatically to the platform detected upon importing the array.

 

Numbered figure captions

...

SubtitleText The Microarray Conversion options page AnchorName

...

Conversion options page

Image Modified

If for some reason you wish to override that selection, then click the Change selection link and select the chip name in the drop-down menu or select New chip… if you would like to upload a different chip annotation (Figure 5).

 

Numbered figure captions

...

SubtitleText Selecting a different probe sequence file AnchorName

...

different probe sequence

...

...

Numbered figure captions
SubtitleText Selecting a different probe sequence file AnchorName different probe sequence

 

In the Select coverage depth section, you can set the nominal read coverage depth for your array. This is by default set at 20 million reads. However, you can adjust this number for better accuracy or if you are evaluating low-expressing genes. If you are comparing the microarray data with a corresponding NGS dataset, you can use this option to scale your data to a more comparable order of magnitude. Take note that setting this to a higher number will result in longer computation times overall.

...