Convert GCT to XLS

A gene-expression matrix may need conversion when a recipient or older application accepts Excel workbooks but not GenePattern data files. Exporting the matrix as .xls makes it editable in legacy Excel-compatible spreadsheet software, but the original GCT file should remain the authoritative source.

What the GCT format is

In the Documents category, GCT normally means Gene Cluster Text, a tab-delimited text format used for gene-expression and other genomic data matrices. GenePattern, Broad Institute tools, and compatible bioinformatics programs read and generate it.

A common GCT 1.2 file contains a version line such as #1.2, a dimension line containing the data-row and sample-column counts, a header beginning with Name and Description, and one tab-delimited row for each gene or other feature. The remaining fields usually contain sample measurements. GCT metadata lines are part of the file structure and are not ordinary spreadsheet headers.

What the XLS format is

XLS is Microsoft Excel's binary workbook format for Excel 97–2003. It supports worksheets, cell formatting, formulas, sorting, filtering, and charts, and can be opened by many spreadsheet applications.

Each XLS worksheet is limited to 65,536 rows and 256 columns. The two GCT identifier fields count toward the column limit, so a matrix with more than 254 sample columns cannot fit in one XLS worksheet. Large matrices generally require XLSX, CSV, or a database instead.

How to convert GCT to XLS

Using LibreOffice Calc

1. Keep a backup of the original sample.gct file.
2. For a clean matrix worksheet, make a copy and remove the GCT version and dimension lines from the copy, or import the file and skip those two lines. Preserve those values separately if they are needed for traceability.
3. Open the copy in LibreOffice Calc. If Calc does not recognize the extension, rename the copy to sample.txt; this changes only the name, not the tab-delimited content.
4. In the text-import dialog, choose Separated by, enable Tab, and disable other separators. Check that Name, Description, sample names, and measurements occupy separate columns.
5. Format gene identifiers and other identifier fields as text when they contain leading zeros, long numeric-looking strings, or characters that Calc might reinterpret.
6. Choose File → Save As, select Excel 97–2003 (*.xls), and confirm the legacy-format warning.

Calc is a practical local option because it reads tab-delimited text and writes legacy XLS without requiring an intermediate conversion service.

Using Microsoft Excel

1. Use a copy of the GCT file and rename it to .txt if Excel will not display the .gct file in its open or import dialog.
2. Choose Data → From Text/CSV, select the file, and set the delimiter to Tab.
3. Remove or skip the first two GCT structure lines for the matrix worksheet. Store the version and dimensions in separate cells or a separate worksheet if they must be retained.
4. Set identifier columns to text before loading when possible, then compare sample values and representative gene IDs with the source file.
5. Choose File → Save As, select Excel 97-2003 Workbook (*.xls), and accept the compatibility warning.

Using a repeatable script

For batch processing, parse the GCT table after its two structural lines and initially keep every field as text. This avoids unwanted conversion of identifiers, dates, and long values.

import pandas as pd

df = pd.read_csv('sample.gct', sep='\t', skiprows=2,
                 dtype=str, keep_default_na=False)
df.to_excel('sample.xlsx', index=False)

This code creates XLSX, not XLS. Open the result in Calc or Excel and use File → Save As → Excel 97–2003 (*.xls). Convert selected measurement columns to numeric only when calculations are required. If preserving GCT metadata, read the first two lines separately and write them to a metadata sheet.

Online conversion options

There is no broadly supported, dedicated online GCT-to-XLS service that reliably understands GCT version and dimension lines. Generic conversion sites may treat the file as undifferentiated text, shift the table header, or alter numeric values. Gene-expression data may also be confidential, so local Calc, Excel, or a controlled script is safer.

An online spreadsheet can handle a non-sensitive, small matrix as a fallback: remove the first two GCT lines in a copy, upload the resulting tab-delimited text to Google Sheets or Excel for the web, verify the imported columns, and export an Excel workbook. These services normally export XLSX rather than legacy XLS, so the final XLS save still requires desktop Excel or LibreOffice.

Quality and compatibility limits

• Putting #1.2 and the dimension line into workbook cells preserves their text but does not make the workbook a valid GCT file.
• Spreadsheet software may convert gene identifiers, dates, leading zeros, long integers, and scientific notation. Compare representative cells with the original after export.
• Formatting and formulas added to the workbook are not part of the GCT source and will disappear if the workbook is regenerated from that source.
• GCT matrices exceeding XLS worksheet limits must be exported as XLSX, split across worksheets or files, or stored in another tabular system.
• Saving measurement fields as text protects exact input values but prevents normal spreadsheet arithmetic until the required columns are explicitly converted to numbers.