Scientists often develop lists of genes, probes, transcripts, SNPs, and genomic regions of interest from analysis tools, research papers, and databases. Using Partek® Genomics Suite®, these lists can be integrated with genomics data sets, analyzed with powerful statistics, and visualized for new insights.
This tutorial will illustrate how to:
The preferred method for importing a generic list of data into Partek Genomics Suite is as a text file.
The File Type section of the Import dialog includes a preview of the text file and import options (Figure 1).
|
The columns in the import file can be separate by a tab, comma, or any other character.
For most applications, the items on the list should be in rows while attributes or values should be in columns. If a list is oriented with items on columns, select Transpose the file to to import a transposed spreadsheet.
|
Selecting Genomic Data will result in a dialog prompt to configure genomic properties including selecting the type of genomic data, the location of genomic features in the spreadsheet, the annotation column with gene symbols, the chip or reference source and annotation file, and the species and genome build. This option should be selected if the text file contains genomic position data or other array/sequencing results.
The Identify Column Labels, Start of Data section (Figure 3)
|
The next step is to identify where the data starts and where the optional header is found. The line that contains the header (if present) must precede the data. If there are lines to be skipped in the file (like comments), they may only appear at the top of the file, before the header line or data begin.
If there are many comment lines at the start of the file, you may need to select View Next 5 Records to get to the row that contains the column header. If you accidentally move past the screen that contains the header or data rows, select View Previous 5 Records.
If there are missing numerical values or empty cells in your input list, insert a special character or symbol (?, N/A, NA, etc.) in the missing cells; you will specify the character in the Missing Data Representation section of the dialog
This is important if the missing value is a number in a column that you plan to use for statistical analysis. The default missing value indicator is ?.
The Preview text encoding section (Figure 4) previews the first five lines of the file, allowing you to check if the text encoding is correct.
|
The final section of the Import .txt, .tsv, or .csv File dialog is Verify Type & Attribute of Data Columns (Figure 5). While data column type and attribute can be modified after import, it is easier and faster to select the proper options during import as multiple columns may be selected during this dialog.
|
If there is an identifier like gene symbol or SNP, the Type field for that column should be set to text and Attribute should be set to label. Numeric values (intensities, p-values, fold-changes, etc.) should have Type set to double and Attribute set to response. The other possible value for Attribute is factor and describes sample data. The user interface is this dialog allows you to select multiple columns at once. The interface controls are detailed in the dialog (Figure 5).
If Genomic Data was selected in the Data Type section, the Configure Genomic Properties dialog will open (Figure 6)
|
|
