Partek ^® Flow ^® accepts custom-made Affymetrix .CEL and Illumina .idat or AVGSignal data generated from Genome Studio files as input. These require an accompanying probe annotation file.
This document describes how to create and import your own custom-microarray annotation files for use in Partek Flow.

Creating Custom probe_tab Files

It is advisable to obtain the annotation files for your custom chip directly from Affymetrix. If for some reason this is not possible, probe_tab files can be created as a tab-delimited text file using any text editor.
They must contain the following information in columns:

• Probe set nameid: unique ID of the  probe
• Probe x: Probe X position on the chip
• Probe y: Probe Y position on the chip
• Probe sequence: sequence of the  probe, all IUPAC nucleotide codes are supported

The first line of the file must be the column headings listed abovebelow. Any mixture of upper and lower case is supported. If you are modifying this from another file, the Probe Id column must be the first column in the file. The order of the other columns does not matter and other columns may be present and any additional columns will be ignored unless they are in conflict with the column names above.

The probe set name Probe id can contain any unique identifier but should generally be the Affymetrix probe name or probe set ID. Note that in some chips, such as the Clariom D arrays, the probe id and probe set id contain different information. If that's the case, identify the column containing unique identifiers and use that as your first column. These names have to be composed exclusively of alphanumeric characters, underscores or hyphens.

...

• probe set name
• probe name
• probe set id
• probe id
• probe set_name
• probe set_id

In cases where both probe set id and probe id are different, Partek Flow will use the identifier present in the first column. Thus, it it absolutely essential that the first column contains unique identifiers.

The probe position columns must be given for both x and y position.
Valid examples of each are:

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Remember to save your modified file with a .probe_tab extension.

Note: Below is the preferred column header example: Probe_id    Probe_x    Probe_y    Probe_sequence

Creating Custom Illumina Annotation Files

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• PROBE_ID
• X.AVG_Signal (where X is the sample name)

In the succeeding linesrows, list each probe ID and its corresponding signal intensity. Save the resulting file with the same sample name (i.e. X.txt where X is the sample name).

Note that the probe IDs must match those present in the accompanying .bgx annotation file. Import these These .txt files must be formatted in either windows- or linux-compatible text file formats. Text files with just carriage returns, such as those generated by Macs are not compatible.

Import the .txt files using the Data tab in your project (Data>Import data>Automatically create samples from files).

Importing Annotation Files into Library File Management

The annotation files can then be uploaded into Partek Flow by going to Settings>Library File Management, selecting the Microarray library files tab and clicking the Add probe sequence button (Figure 1).

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Converting Custom Microarray Files into Aligned Reads

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When prompted to select the probe sequence file, click the Chip name drop-down menu and select the chip name for your custom chip.