There is one row for each gene and one column for each of the samples. The remainder of the data file contains data for each of the genes. (sample N name)Įxample: Name Description DLBC1_1 DLBC2_1. Line format: Name(tab)Description(tab)(sample 1 name)(tab)(sample 2 name) (tab). The third line contains a list of identifiers for the samples associated with each of the columns in the remainder of the file. Line format: ( # of data rows) (tab) (# of data columns) Note that the name and description columns are not included in the number of data columns. The second line contains numbers indicating the size of the data table that is contained in the remainder of the file. Therefore, the first line must be as follows: The first line contains the version string and is always the same for this file format. The GCT format is a tab delimited file format that describes an expression dataset. GCT: Gene Cluster Text file format (*.gct) Note: The GCT & RES expression formats supported by GSEA are identical to those supported by GenePattern. 5.1 RNK: Ranked list file format (*.rnk).3.4 XML: Molecular signature database file format (msigdb_*.xml).3.2 GMT: Gene Matrix Transposed file format (*.gmt).3.1 GMX: Gene MatriX file format (*.gmx).2.2 CLS: Continuous (e.g time-series or gene profile) file format (*.cls).2.1 CLS: Categorical (e.g tumor vs normal) class file format (*.cls).1.4 TXT: Text file format for expression dataset (*.txt).1.3 PCL: Stanford cDNA file format (*.pcl).1.2 RES: ExpRESsion (with P and A calls) file format (*.res).1.1 GCT: Gene Cluster Text file format (*.gct).Due to restrictions imposed by certain Java libraries used by GSEA, the GSEA command line cannot accept file names that contain hypens. When creating files for GSEA, do not use hypens (-) in the file names. When Excel asks if you want to save your changes to this file, select No (you have already saved the file). Excel displays a message warning you that your file may contain features that are not compatible with this format and asks if you want to keep the workbook in this format. To create a tab-delimited text file: select File>Save As, enter the file name in quotes to preserve the the file extension (for example, "p53.gct"), and select "Text(Tab delimited)(*.txt)" as the file type.Be aware that Excel's auto-formatting can introduce errors in gene names, as described in Zeeberg, et al 2004.To create and edit GSEA files, use Excel or a text editor. I mean, this is why the setting exists in the status bar to begin with.Each GSEA supported file is an ASCII text file with a specific format, as described below. This is why being able to have the system detect the convention used by the current file is infinitely better than having to change the Clang_format_fallback Style setting every time. If you are accepting this little inconvenience for existing users than I agree that this is a nicer, cleaner solution.Īnd yes, unfortunately, the formatting of the existing code I am working with changes from file to file, sometimes even within a single file (one method indented with tabs, the other one indented with spaces). Not in a very serious way, as just changing the config once to put the desired explicit values gives back the original behavior (alternatively, he can just enter the desired values in the status bar), but it still requires an action by the user. I thought of this myself, but did not propose it as a possible solution as it is breaking existing behavior. Maybe something like this is already possible, but I did not find out how.įor me, the proposal by looks good, to just add the dynamic values to all other configurations as long as they have not have an explicit value set. This does not seem to work if one wants a different formatting based on existing templates, e.g. When using Clang_format_fallback Style "Visual Studio", the extension respects what is selected in the "Select indentation" part of the status line, using either spaces or tabs as indentation method, with the selected size for every indentation level, and the possibility of auto-detecting the best setting for the existing file.
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