Frequently Asked Questions about NTSYSpc
  1. What is the current version of NTSYSpc?  Version 2.2 was initially released Sept. 2005. Note: there will be free service releases (with numbers and letters like 2.20a) that add new features and fix problems that were discovered after the initial release (there will probably be several updates as problems are reported in the new version). Please check the Updates page to see if a more recent release is available. Click on the help|About menu in NTSYSpc to check what release you currently have installed. While you do not have to uninstall the old version, it is better to uninstall the old version before the new one is installed. The uninstall process will not remove any of your data files.
  2. Is there a tutorial available? While there is no tutorial guide available, the printed Getting Started Guide provided with the program gives a step-by-step example. This guide is also available as an Acrobat PDF file on the distribution CD. It can also be downloaded here (340K). The help file contains step-by-step examples of using NTSYSpc for both a UPGMA cluster analysis and a principal components analysis. The main problem new users seem to have is due to the expectation that there is a single button to click to perform an entire analysis. Unlike many statistical packages, most analyses require one to go through a number of steps. While less user-friendly, this design makes many more types of analyses possible by combining the modules in various ways. There is also a copy of the install guide included with the software.
  3. End of file or other problems reading a data file? This is the most frequently reported problem. This almost always is due to an error in preparing the data file. Common problems are miscounting the number of row or column labels or miscounting of the number or rows or columns in the matrix itself. Please double-check your files! Sometimes it helps to have someone else look at your file.
  4. Error codes? Did you receive an error message that consists of just a numerical code (such as "Error 103")? We try to suppress these internal error codes and replace them with meaningful messages. Some still get through. The help file has a topic that lists all of the error codes.
  5. Does NTSYSpc read Excel files? NTSYSpc 2.0 did not read Excel files directly. One had to use the NTedit program to import the file and save it as a standard NTS file and a copy of the Excel program was required to be on your computer. Version 2.1 solved that problem by reading Excel files directly from both NTedit and NTSYSpc. As of release 2.10m all types of matrices can be read (not just rectangular as in previous releases).  A limitation at present is that only a single matrix can be read from an Excel file (a way around this limitation is to save your Excel spreadsheet as a CSV format file. Note that Excel and CSV files must start with NTSYSpc header information. There can be optional comments and row and column labels. There must be a line that tells NTSYSpc how many rows and columns to expect.  The matrix header line for Excel files in NTSYSpc ver. 2.0 was slightly different from that of the standard NTS files. In version 2.1 it is now the same as in the NTS files except that the suffix codes 'L', 'B', and 'E' must not be used. The NTedit program can now also write CSV files. Excel 2007: this version of Excel uses a totally new file format (*.XLSX) that is compatible with NTSYSpc version 2.21c and later. As of version 2.20r, NTSYSpc can read XLS files that Excel 2007 writes in its "compatibility mode." One can also save a spreadsheets as a CSV files for input to NTSYSpc.
  6. Problems using NTSYSpc? Be sure to check whether a new service release is available. You will need a password (contact Exeter Software) and your present registration serial number. updates The Updates section of the help file lists the additions, changes, and problems fixed in each release of NTSYSpc.
  7. Why does MDSCALE always stops after just 5 iterations even though the solution is not very good? The default value for "Maximum stress ratio" was set at "0" (fixed in release 2.10K). You should change that value to something like "0.999".
  8. Computations of similarity/dissimilarity values seems to 'blow up'? If a cluster analysis results in no structure and the range of similarity values going from 0 to 0 or from 1 to 1 then there may be a problem with the missing value code being set when you did not expect it. Whether or not the missing value code is set is mentioned in the listing output. In NTedit make sure the missing value edit box is blank (not a '0') if there are no missing values in the data.
  9. Batch codes for MOD3D and MXPLOT. The batch code parameters for specifying the variables was changed from that in version 1.80 of NTSYSpc. They now use X, Y and X, Y, Z rather than I, J and I, J, K.
  10. Data size limits? Most modules in NTSYSpc do not have explicit dimension limits for objects or variables. The limitation will be disk space and time. Larger amounts of RAM will speed up to computations for very large datasets. With the present capacity and power of modern PCs, a data set with  a few hundred samples or variables is considered a small dataset for most computations. However, the MDSCALE module must manipulate many matrices simultaneously and hence is more limited in the size of the matrix it can handle (512 variables is the maximum).  The canpls module is currently limited to 255 variables.
  11. Why are only the first 30 OTUs are shown in the dendrogram? By default, a maximum of 30 OTUs are displayed on each page of the dendrogram. To display additional pages or to change the number of OTUs/page, right-click on the plot to bring up the options window. You can change many aspects of the plot including the fonts used to display the titles and OTU labels. In version 2.1 you can use the PageUp and PageDown keys to scroll through the other pages. You can also use the "+" and "-" keys to change the number of OTUs per page.
  12. Can NTSYSpc use the "," character as a decimal separator? Yes, version 2.20r and later allow a user to specify the decimal character. In the main window, click on Options and then Configure. In the entry form you may change the default "." to a ",". Changing this will also change the separator used in CSV files to a semicolon ";".
  13. A problem was found in the MULREG module. For regression through the mean, the numerator degrees of freedom for the overall test is k+1 rather than k (where k is the number of independent variables). This was fixed in version 2.10x. Please update your copy to that version if you plan to use that module.
  14. How should I cite NTSYSpc in a publication? You can use the following format: Rohlf, F. J. 2018. NTSYSpc: Numerical Taxonomy System, ver. 2.21r. Applied Biostatistics. Port Jefferson, NY 11777. [substitute, of course, the exact version number you have and its copyright date from the Help|About window.]
  15. What happened to the ntsys.ini file? Release 2.20w has made an important change in the placement of the ntsys.ini file. Earlier versions placed it in the same directory as the ntsys.exe file. This caused problem on some computers (such as student labs where strict constraints are placed on where a user can store files). Release 2.20w now places the file in an ntsys subdirector under the current user's My Documents directory. Note there is a -N runtime option that will cause NTSYSpc to place in the same folder as the ntsys.exe file. This option may be needed on computer in, for example, student labs where the documents folder is protected from modification by users.
  16. Why do the numbers in the output file seem to be off by a factor of 10? NTSYSpc uses an exponential format in the output files so as to preserve as much accuracy as possible. The numbers are in the format x.xxxxxxxxxeyyy where the "yyy" indicates the power of 10 to multiply the "x.xxxxxxxxx". Thus, for example, "2.00000000000000E-001" corresponds to "0.2", "1.05477465476420E+002" corresponds to "105.477465476420", and "1.02237799184597E+000" to "1.02237799184597" .
  17. Is there a step by step guide to the installation of NTSYSpc? Yes, a guide is available as a PDF file here.
  18. Are there youtube or other tutorials? Yes, several users have posted vido tutorials or other information. Some are for older versions but the principles of how to use NTSYSpc has not changed much. Some links are given below. Links to some papers using NTSYSpc are also given.

This file was last modified on 18 June 2023. SiteLock