## FAQ - Frequently Asked Questions

**Please browse from the following list of FAQ items.**

**Topic: Importing / Exporting**

• How do I concatenate multiple files into a single DataSet?

• How do I create a multivariate image from separate images?

• How do I export PCA scores and loadings to a text file (to read into MS Excel,

for example)?

• How do I import three-way data into Solo or PLS_Toolbox?

• Why can't I import a Horiba NGC file on my 64-bit computer?

• Why can't SPCREADR read multiple files I've selected?

• Why do some Excel files fail to import?

**Topic: General**

• Can I do PARALIND in PLS_Toolbox?

• Can I install PLS_Toolbox (or Solo) on more than one PC, such as on my desktop

and laptop computer?

• Can I use multiple class sets (categorical variables) together in a SIMCA,

PLSDA, or LDA model?

• Can you give me more information on the R-Squared statistic?

• Convergence of PARAFAC. How much variation between models is expected a

particular PARAFAC is fit multiple times with the same settings?

• Does the software stop working if my maintenance expires?

• How and where do I report a problem with PLS_Toolbox?

• How are RMSEC and RMSECV related to R2Y and Q2Y I see in other software?

• How are T-contributions calculated?

• How are the ROC curves calculated for PLSDA?

• How are the error bars calculated for a regression model and can they be related

to a confidence limit (confidence in the prediction)?

• How can I improve performance with PLS_Toolbox and Matlab on the Mac platform?

• How do I assign classes for samples in a DataSet?

• How do I build a classification model from a class set other than the first?

• How do I choose between the different cross-validation leave-out options?

• How do I cite/reference Eigenvector?

• How do I extend the trial period of a demo licence?

• How do I interpret the ROC curves and Sensitivity / Specificity plots from

PLSDA?

• How do I make a DataSet backwards compatible?

• How do I obtain or use a recompilation license for PLS_Toolbox?

• How do I use the "custom" cross-validation option?

• How is the prediction probability and threshold calculated for PLSDA?

• I keep getting "out of memory" errors when analyzing my data. What can I do?

• I keep getting an error with Plotgui "Unrecognized Property or Mode Keyword

'functionname'". What should I do?

• Nonnegativity (PARAFAC, PARAFAC2, Tucker): Why do I get negative scores when all

modes are set to nonnegativity?

• Some of the items in my plots and figures don't appear correctly or are cutoff

by the figure.

• The toolbar buttons in the Analysis figure don't show up correctly after I

update to Matlab R2006a. What can I do?

• What are "Relative Contributions"?

• What are the "Reduced" T^2 and Q Statistics?

• What are the units used for RMSEC and RMSECV when cross-validating PLSDA

models? Why do the cross-validation curves look strange for PLSDA?

• What can I do if I get a java.lang.OutOfMemoryError error?

• What do the four Fit/Unique Fit statistics mean in MCR and PARAFAC models?

• What internal tests are used to select "suggested" number of PCs?

• What is PLS1 vs PLS2 and how do I create separate PLS1 models when I have a

multi-column y-block?

• What is the difference between a loading and a weighting?

• Why are some axis labels and titles on my axes upside-down when I'm viewing

images in MIA_Toolbox?

• Why can't I recompile the PLS_Toolbox functions?

• Why do I get the warning/notice "Missing Data Found - Replacing with "best

guess" from existing model. Results may be affected by this action."

• Why does PLS_Toolbox have a "boxplot" function that conflicts with the Mathworks

Statistics Toolbox function of the same name?

• Why does R2014b give me "Error using matlab.ui.Figure... Cannot convert double

value to a handle" (or similar)?

• Why is the confidence limit on scores different in PLS_Toolbox after version

3.5.2?

**Topic: Command-Line**

• After I upgraded PLS_Toolbox, my scripts which used MCR no longer work.

• Do I have to specify all the options to a function or only the ones that are

different from the defaults?

• How are the Q-residuals and Hotelling's T^2 (T

^{2}) values calculated

for PLS models?

• How do I automate PCA analysis for multiple images?

• How do I calculate my own T

^{2}and Q limits?

• How do I calculate scores from a PLS or PLSDA model?

• How do I change the default options for a function?

• How do I interpret the Misclassification results reported by crossval?

• How do I make PlotGUI send its plot to a new figure and not overwrite the

current figure?

• How do I make the plotscores commands shown at the end of the VARIMAX demo work?

• How do I manually calculate the limits for scores?

• How do I retrieve and display predictions from a model structure in the command

window?

• How do I specify all options on the same line that contains the call to a

function?

• How do I use specific known pure component spectra with MCR (Multivariate Curve

Resolution)?

• How does PCA cross-validation work in PLS_Toolbox and Solo and how do I set up

the command-line options to best use it?

• I get an error message when I run NCROSSVAL which says that it can not find

NPROCESS or that there are too many inputs into NPREPROCESS

• I get an error message when I use plotscores with a scores matrix.

• Where do I find a description of the parafac2 constraints?

• Where do I find the regression vector (B) and regression intercept

(B

_{0}) for a PLS or PCR model?

• Where is the conpred1 function?

• Why do I get an error saying "Too Many Output Arguments" when using the

Mathworks' Neural Networks interface?

• Why do I get different cross-validation results from the command-line crossval

routine compared to the Analysis window?

• Why do I get different results when I preprocess before doing my

cross-validation vs. doing preprocessing inside crossval?

• Why does the PCAENGINE change the sign of the loadings returned by SVD?

• Why is my model built using command line functions different from the same one I

built in Analysis GUI?

**Topic: Manual**

• The example on page 14 of the PLS_Toolbox manual (loading labels into the

DECOMPOSE GUI) gives the error "Number of rows must = number of columns of

loaded data - no labels loaded"?

• What kind of training material comes with a PLS_Toolbox or Solo license?

• Where can I find the current manual?

• Where can I find the electronic version of the documentation?

• Why can't I make the MCR example on page 92 of the PLS_Toolbox manual work?

**Topic: GUI**

• After I make a selection in IMAGEGUI or PLOTGUI, some of the menus disappear.

• How do I add confidence ellipses around groups of samples?

• How do I add my own preprocessing methods to the Preprocess GUI?

• How do I change the default plots created by the Scores button in the Analysis

GUI?

• How do I change the font size for all labels on a plot (at once)?

• How do I change the limit on how many rows or columns I can access in a plot

(Plot Controls)?

• How do I enable the PLS, PCR and/or SIMCA analysis methods in the Analysis GUI?

• How do I export PCA, PLS or PCR predictions or scores to a text file or another

program?

• How do I limit my analysis to a sub-range of the variables in my data?

• How do I load labels, classes or an axisscale for my data in the Analysis GUI?

• How do I make a prediction on new data using the Analysis or Regression GUI?

• How do I see and/or include more than 20 factors in a PLS or PCR model when

using Analysis GUI?

• How do I view a table of predictions, scores, or other data?

• I am getting out of memory errors when using preprocessing in Analysis GUI - how

do I analyze this data within the GUI?

• I am unable to print scores or loadings plots, or I am unable to print figures

created by PlotGUI.

• I get an error "Too many output arguments" when starting the Analysis GUI (or

similar)

• I get an error in PlotGUI "Invalid object handle" (error in plotds with

MIA_Toolbox installed)

• I get the error "no PixelPosition property" when starting Analysis GUI.

• What is the "Figures" window used for and how do I keep all figures in the same

window?

• Why do I get a "no pixel position" error when starting Analysis GUI in

PLS_Toolbox 4.2 with Matlab 7.0.1?

• Why does a cumsum error occurr when replacing missing data in Matlab 6.1 in the

GUI (PCA mode)?

• Why does the "Select" button stay pressed after I make a selection?

**Topic: Installation**

• "Error using figure UIJ_AreThereWindowShowsPending - timeout waiting for window

to show up"

• Can you describe an easy way to switch from one version of PLS_Toolbox to

another?

• Do any PLS_Toolbox functions conflict with the Mathworks Toolboxes?

• GUIDE (the figure editor) fails in Matlab 7.0 and higher with PLS_Toolbox at the

top of the path

• How do I calculate / verify the MD5 or SHA1 hashes on a file?

• How do I install PLS_Toolbox on two different versions of Matlab?

• How do I install multiple Eigenvector products?

• How do I switch from a demo version of PLS_Toolbox or Solo to install and use a

new purchased version?

• How do I use PLS_Toolbox or Solo with a license server when I don't have access

to the network?

• How is PLS_Toolbox installed with a network copy (site-license) of Matlab?

• I bought a copy of PLS_Toolbox but I am getting warnings about the license

expiring or my license has expired.

• I get a warning saying the evriio.p file was p-coded from an old MATLAB version.

• I get an "Invalid property found" error when installing, what should I do?

• I get the message "Path cannot be saved" and don't seem to have permission to

write to my 'pathdef.m' file. What can I do to keep from having to install

PLS_Toolbox each time I start Matlab?

• I get warnings for overloaded 'true' and 'false' functions in PLS_Toolbox.

• I loose my floating license if I am inactive in Matlab. How do I keep a license

checked out?

• I ran the PLS_Toolbox installer and a menu asks to start Matlab and run a

script, but Matlab never starts. How do I finish the installation?

• I'm having problems installing and using PLS_Toolbox with Mac OS X.

• I'm having trouble installing Solo on a Mac.

• If we purchase a floating license does the floating license need to be added to

the Matlab floating license, or can it be served by a separate license server?

• Is PLS_Toolbox compatible with Matlab 2010b? What are the warnings I get?

• Is PLS_Toolbox compatible with Matlab 2012b? What are the warnings I get?

• PLS_Toolbox version 3.5.3 doesn't install in Matlab version 6.1 without true.m

and false.m, where can I get them?

• Problems installing PLS_Toolbox on Matlab 7.0.

• Solo fails with "mclstart: Unable to initialize PLS_toolbox library check for

missing plstoolbox.ctf file" or requires re-installation each startup.

• Solo_Predictor gives the error "Error using object. Attempted to access out(1);

index out of bounds because numel(out)=0."

• Some or all of the PLS_Toolbox functions do not work.

• Staring Solo on Fedora Linux I get the message: "SELinux is preventing

.../EVRI_lib" from performing execstack access on a process"

• Trouble downloading, installing, starting, or running Solo.

• What is the version compatibility between PLS_Toolbox and Matlab?

• What's a good way to add or remove PLS_Toolbox from my path?

• What’s the best way to install Solo/PLS_Toolbox in a classroom?

• When installing Solo or other stand-alone I get a warning saying "Could not

write updated MCR_INHIBIT_CTF_LOCK to HKLM"

• When starting Solo I get the message "The application has failed to start

because its side-by-side configuration is incorrect."

• Why am I unable to make changes to the path in MATLAB on Windows 7?

• Why do I get "attempt to run script as a function" errors after I install

PLS_Toolbox?

• Why do I get an error "Missing operator, comma, semicolon, or white space."

after installing the toolbox?

• Why do I get an error that my license code is not valid?

• Why do I get the error "Reference to non-existent field 'nobs'"?

• Why do I have to reenter my license code every time I start?

• Why do I need to run EVRIINSTALL when installing PLS_Toolbox?

• Why does my floating license return the error "License server cannot be run on

the same computer as this application" (or code -3) when I try to check out a

license?

• Why is the PLS_Toolbox help information not available in my Matlab help window?