topic Re: Friedman test on JMP? in Discussions

Friedman test on JMP?

beginners_luck — Fri, 16 Nov 2012 12:14:23 GMT

Dear all,

I am fairly new in using the JMP software, and as far as I can see there is no function in the programme for using the Friedman test? I have a non-normal distribution of my different sets of values (more than three groups) and is opting for a non-parametric test. That is, I had like to test a 2-way type of test (as ANOVA). Wilcoxon test is insufficient since it is a one-way test.

Do anybody know how I will deal with is problem? Is there another test to perform instead of Friedman test?

Best regards,

Re: Friedman test on JMP?

stevedenham — Fri, 16 Nov 2012 13:07:42 GMT

If you can't find the Friedman test in the menus (and I have no idea whether you can or not, since I am not a JMP user), you could rank transform your data, and use a two-way ANOVA on the ranks. In SAS, this is available in PROC FREQ, so I would check the JMP documentation for the possibility of doing Friedman's test in that manner.

Steve Denham

Re: Friedman test on JMP?

beginners_luck — Fri, 16 Nov 2012 15:06:50 GMT

Thanks for the help. Although the Friedman test seem not listed in the JMP menu or elsewhere in the programme. Perhaps I need to perform it on SAS if JMP doesnt conduct these tests.

Best regards,

Jim

Re: Friedman test on JMP?

Jeff_Perkinson — Fri, 16 Nov 2012 15:18:47 GMT

Hi Jim,

Friedman's test is not supported directly in JMP but, as Steve points out you can do this by calculating the ranks within each block and then doing a two way ANOVA on ranks using Fit Y by X (treating one of the effects as a blocking variable).

Computing the ranks within block is easy in JMP. Just use the Distribution platform with your original response as Y and your blocking variable as a By variable. Then, in the resulting report, hold down the Ctrl key and click on the little red triangle at the top of one of the histograms and choose Save->Ranks. You'll get a new column in your data table with the ranks within levels of your blocking variable.

I hope that helps!

-Jeff

Re: Friedman test on JMP?

beginners_luck — Sat, 17 Nov 2012 20:03:20 GMT

Thank you very much Jeff. However I am not sure I have found what I am looking for: 2-way ANOVA. It seem in the end I receive only one-way ANOVA data in the output file. This is what I did: First, I conducted Distribution analyses and rank transformed data from one of the traits I have studied (Y) accoridng to its randomized block design, i.e. block (By). The data was saved as ranks (six rank/block data compiled into one column of the Jmp data sheet), and next I analyzed the rank transformed trait with Fit Y by X: Y as rank data, and for X I used treatment as a variable. However, in the output file I only see one-way ANOVA data!

Have it been conducted the wrong way? Or is the data to be find somewhewre within the output file?

Thankful for input in this matter!

Best regards,

Jim

Re: Friedman test on JMP?

stevedenham — Mon, 19 Nov 2012 12:45:26 GMT

For X, you must specify both treatment and block (but not their interaction) to get Friedman's test.

Steve Denham

Re: Friedman test on JMP?

Jeff_Perkinson — Tue, 18 Oct 2016 20:04:36 GMT

Hi Jim,

You need to specify your Blocking variable in the Block role in the Fit Y by X dialog:

-Jeff

Re: Friedman test on JMP?

beginners_luck — Tue, 27 Nov 2012 00:11:19 GMT

Hej!

Thanks for all the help. I will get into the matter and hoipefully be able to solve it soon. I will be back with some hopefully successfull results.

Sorry for late reply, I am busy with some lab work.

Sincerely,

Jim

Re: Friedman test on JMP?

beginners_luck — Thu, 29 Nov 2012 01:13:29 GMT

Hi again!

Thank you. Unfortunately, I havent sorted it out yet. However, perhaps I need to redo the ranks (distribution analyze to save ranks), since when I run the Fit y by x-analyses a post shows up saying "Blocking ignored because cell counts were unequal." After that I excluded a few replicates that contained some empty cells thinking this could be the reason of unequality, saved it as ranks and ran it in fit y by x, but the unequality still remain and the post shows up again). Could it be that there are some species having 6 replicates and, now some are having 5 replicates? All replicates however are equal in number of treated samples (i.e. control and treated). Is this posing a problem for conducting the Friedman test?

In my Fit y by x-runs I used, in the specification model, the trait values as response Y, and the treatment and block number for factor X and block. I even switched the treatment and block number for those two specifications. But in addition to receiving the previously mentioned post sign it did not display any data or relevance (2-way ANOVA p-values for example).

Also. So far. The ensuing output file doesnt (never) display any two-way ANOVA data, but instead the output file (as always) have the caption of One-way ANOVA. How exactly can you see whether your Friedman test is shown or not on the output file? I dont think there is a caption saying, for example, nonparametric two-way ANOVA in the fit y by x-output?

If anyone have a clue on this please drop a line or two! I am not giving up on this one (yet).

Best regards,

Jim

Re: Friedman test on JMP?

stevedenham — Thu, 29 Nov 2012 13:05:32 GMT

Give up NOW on Friedman's Test. It only applies when there is an equal number of observations in each block. Think about it--consider two blocks, one with five observations and one with ten. The mean of the first block is 3, of the second 5.5. You automatically have a difference, so the null hypothesis cannot be true, thus any p values are, well, bogus. This means you can't just rank transform your data by block, and get anything meaningful. JMP protects you from doing this, and issues the error message.

So it is time to stop, and reconsider your analysis approach. You say you have non-normal data. That may be, but the assumptions of ANOVA are that the errors are normally distributed. Have you examined them? What does the error distribution look like? Is it amenable to transformation? It is probably time to consult with someone face-to-face to try and answer these questions. Then, an appropriate analysis plan can be devised.

Steve Denham

Re: Friedman test on JMP?

beginners_luck — Thu, 06 Dec 2012 19:13:13 GMT

Hi again!

Yes I have finally put the testing to rest. I may give the Friedman test a go later on, but on SPSS. A colleague of mine told me are attemtping to conduct the Friedman test on SPSS.

But thank you for all the help and good advices.

Best regards,

Jim

Re: Friedman test on JMP?

jlaborde — Thu, 02 May 2013 07:05:41 GMT

I am also getting the error, "Blocking ignored because cell counts were unequal" when I try to do a simple ANOVA, despite the fact that all my blocks have an equal number of observation. Were you ever able to figure this out? Thanks!

Re: Friedman test on JMP?

beginners_luck — Thu, 20 Feb 2014 18:53:33 GMT

Hi,

I am afraid not. I gave the test up some time ago. But I may look into it again as I have some new data, soon, that will be analyzed statistically. I will update on this issue if Friedman is of interest again.

Best regards,

Jim

Re: Friedman test on JMP?

maria — Sat, 24 Dec 2016 14:43:42 GMT

This was very helpful but when I chose save ranks I only have about half my data that has a rank

Re: Friedman test on JMP?

Reinaldo — Wed, 09 May 2018 20:56:33 GMT

Hi,

How can I run that Friedman's test for a repeated-measures design, please?

Let me know the step procedures.

Thank you.

Re: Friedman test on JMP?

maria — Wed, 09 May 2018 21:04:56 GMT

I asked the same question and JMP support replied this, which works

JMP has many nonparametric tests built in. The Friedman’s test is not directly available in JMP, but you can transform your data into ranks in JMP to create this test as just a 2-way ANOVA on the ranks (using the blocking factor and your other factor as the two additive factors). There is a blog about this (and arguing, at the end, why you might not want Friedman’s test in some cases) here:https://community.jmp.com/t5/Discussions/Friedman-test-on-JMP/td-p/5974.

It is a problem if you have ties, which may be why your data are not normal in the first place. People often forget that alhtough non parametric tests don't assume that the data are normal, these tests still have assumptions. Hope this helped

Re: Friedman test on JMP?

Reinaldo — Wed, 09 May 2018 21:57:22 GMT

Hi Maria,

Thank you for your reply and link. I took a look at those posts, but as I understood that problem didn't refer to a repeated-measures design, did it?

When we face a repeated-measures design, in general, the stats procedures change due to the peculiarity of that design.

Jeff (@Jeff_Perkinson), do you have any suggestion to solve this problem, please?

Thank you very much.

Re: Friedman test on JMP?

maria — Wed, 09 May 2018 22:44:17 GMT

Once you have the ranks, you are essentially doing a repeated measures on the ranks - so you are transforming the data and conducting the RM analysis on the ranks. That is basically what a Friedmans test is doing under the hood

Re: Friedman test on JMP?

Reinaldo — Thu, 10 May 2018 17:59:13 GMT

Hi Maria,

You mean using Fit Model for ranks in order to perform the RM analysis. However, in the last posts I saw using Fit Y by X for calculating the blocks. Perhaps, I need to do it first and then go to the Fit Model. As I understand, RM can be evaluated in the Fit Model only.

Thank you.

Re: Friedman test on JMP?

34South — Thu, 31 Jan 2019 13:31:11 GMT

I realise this is an old discussion, but I found it most helpful. I have been able to successfully implement it but have the following question:

For evaluating the impact of both variables on the outcome variable, I assume one must test each separately, using ranks created using both but alternating them between blocking and dependent roles. However, how does one determine interaction between these two variables? Luckily I was able to transform my data successfully and perform a two way ANOVA using the Fit Model platform. Is this a limitation of the Friedman test?