| Author | Message | ||
     kanchan sonkar (kanchi2209) New member Username: kanchi2209 Post Number: 4 Registered: 4-2010 |
Hello Sir, Thank you very much for the responce and the references.. as you recommended I have downloaded SIMCA-P+ software and will use this for learning purpose..but I would like to implement OPLS-DA in MATLAB.... I got only Ref 1, it will be very helpful if you provide these two references. Thank you again.. Kanchan | ||
| Johan Trygg (trygg) New member Username: trygg Post Number: 2 Registered: 1-2006 |
Hi, I would recommend that you download a fully working demo of SIMCA-P+ software to do your OPLS-DA modelling (www.umetrics.com), a direct link is http://www.umetrics.com/Content/Downloads/SIMCA-P%2B_12.0.1_Demo.ept. Then, have a look at the following references that contains the workflow (ref 1) and the underlying method theory (ref 2 & 3) of the method. If you want, I can email you the electronic pdfs. Ref 1.) Wiklund S, Johansson E, Sj�str�m L, Mellerowicz EJ, Edlund U, Shockcor JP, Gottfries J, Moritz T, Trygg J, Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models, ANALYTICAL CHEMISTRY 2008 80, 1:115-22 Ref 2.) Bylesj� B, Rantalainen M, Cloarec O, Nicholson JK, Holmes E, Trygg J, OPLS Discriminant Analysis, Combining the strengths of PLS-DA and SIMCA classification, JOURNAL OF CHEMOMETRICS, 20 (8-10), 341-351 2006 Ref 3.) Trygg J, Wold S. Orthogonal projections to latent structures, O-PLS. JOURNAL OF CHEMOMETRICS, 2002; 16: 119-128 If you still want to do it with Matlab code, then you get enough info by reading the original reference (Ref 3) and implement it yourself. There the algorithm is presented in detail for single-Y, which you can use for the two-class discriminant analysis if you construct a binary y-variable (1/0) where 0 defines the control class. See Ref 1, if you want more info on this. Cross-validation and other diagnostic tools, including plotting and prediction capabilities are already at hand in the SIMCA-P+ software so it makes it easier. Good luck, and let me know if you need those references, Regards, Johan Trygg Ume� University, Sweden | ||
| venkatarman (venkynir) Senior Member Username: venkynir Post Number: 100 Registered: 3-2004 |
There are good number of Publicaiotn in OPLS-DA. use CSIR journal search , you can get very good publicaiton with code. Chemo.Ins, Analyst, Talanta etc.. are good journal to probe. | ||
| kanchan sonkar (kanchi2209) New member Username: kanchi2209 Post Number: 3 Registered: 4-2010 |
Hi.. thanx..but the thing is that I want to use OPLS-DA only because my further analysis is dependent on its result. I am searching but not getting any thing releted to this in Matlab, but people have used OPLS-DA in Matlab. Do you have any idea about this?? | ||
| venkatarman (venkynir) Senior Member Username: venkynir Post Number: 99 Registered: 3-2004 |
Good ; In the case of DA latest technique is SVM(support Vector Machine ). There ae tool box in Matalab for SVM. You may get good result. | ||
| kanchan sonkar (kanchi2209) New member Username: kanchi2209 Post Number: 2 Registered: 4-2010 |
The data which I am using is NMR spectroscopic data of infected and control samples. I want to discriminate between infected and control, on the basis of differences which appear in both the cases, as is done using other chemometric tools like PCA. Instead of using PCA or any other method I would like to use OPLS-DA as I mentioned in my previous post. That is why I am asking for Matlab code for this. | ||
| venkatarman (venkynir) Senior Member Username: venkynir Post Number: 98 Registered: 3-2004 |
Kindly mention the analysis .Your questions is vague . Better emerging DA analysis are available as a tool. Nothing is mentioned about your data /analysis | ||
| kanchan sonkar (kanchi2209) New member Username: kanchi2209 Post Number: 1 Registered: 4-2010 |
HI.... I am doing some analysis in which I have to incorporate OPLS-DA method. For the analysis, I am using MATLAB Version 7.8. Can anyone provide me the codes for OPLS-DA. Thanx in advance |