+ Reply to Thread
Page 1 of 2 1 2 LastLast
Results 1 to 15 of 16

Thread: Chi-square Vs. Fisher's exact test (FET)

  1. #1
    Points: 5,591, Level: 48
    Level completed: 21%, Points required for next Level: 159

    Posts
    24
    Thanks
    0
    Thanked 0 Times in 0 Posts

    Chi-square Vs. Fisher's exact test (FET)




    I'd really like to have a statistician answer this because I cannot find the answer anywhere. Perhaps you could be kind enough to direct me towards a text that would answer this.

    Given the general rule of thumb that FET is used when the cell count is less than 5 and that computers have made statistical calculations very easy, why not use the FET over chi-square for most if not all applicable analyzes. Essentially, what are the statistical advantages of using chi-square over FET?

    Thank you

    Any one able to shed some light on this for me?
    Last edited by helpwithstats; 08-22-2008 at 08:13 AM.

  2. #2
    Points: 5,591, Level: 48
    Level completed: 21%, Points required for next Level: 159

    Posts
    24
    Thanks
    0
    Thanked 0 Times in 0 Posts
    *bump thread*

  3. #3
    Dark Knight
    Points: 1,890, Level: 25
    Level completed: 90%, Points required for next Level: 10
    vinux's Avatar
    Posts
    1,880
    Thanks
    45
    Thanked 190 Times in 157 Posts
    Hi,
    It’s appropriate to use Fisher’s exact test, in particular when dealing with small counts. The chi square test is basically an approximation of the results from the exact test.
    If you do chisquare test for small counts you may come up with erroneous results because of the approximation.

    And it is difficult to calculate Pvalue for FET for large counts.
    In the long run, we're all dead.

  4. #4
    Points: 5,591, Level: 48
    Level completed: 21%, Points required for next Level: 159

    Posts
    24
    Thanks
    0
    Thanked 0 Times in 0 Posts
    Thanks for the clarification. I suppose with computers doing most of the calculations, fishers can be used in most instances.

  5. #5
    Points: 3,489, Level: 36
    Level completed: 93%, Points required for next Level: 11

    Posts
    154
    Thanks
    0
    Thanked 0 Times in 0 Posts
    Actually fisher gets quite unwieldy pretty fast. On a side note I read a paper about 6 different ways to analyze a simple two by two table that was fascinating. I always wish I had bookmarked it. There are a few subtle assumptions involved in these things that are easily overlooked and result in slightly different p-values.

  6. #6
    Points: 5,591, Level: 48
    Level completed: 21%, Points required for next Level: 159

    Posts
    24
    Thanks
    0
    Thanked 0 Times in 0 Posts
    if you ever find that website, please post it so i can take a look.

  7. #7
    Dark Knight
    Points: 1,890, Level: 25
    Level completed: 90%, Points required for next Level: 10
    vinux's Avatar
    Posts
    1,880
    Thanks
    45
    Thanked 190 Times in 157 Posts
    Quote Originally Posted by helpwithstats View Post
    Thanks for the clarification. I suppose with computers doing most of the calculations, fishers can be used in most instances.
    Hi,
    Go through following links
    http://en.wikipedia.org/wiki/Fisher_exact_test
    http://www.quantitativeskills.com/si...s/fishrhlp.htm
    http://faculty.vassar.edu/lowry/fisher.html
    http://udel.edu/~mcdonald/statfishers.html

    Regards
    Richie
    In the long run, we're all dead.

  8. #8
    Points: 5,591, Level: 48
    Level completed: 21%, Points required for next Level: 159

    Posts
    24
    Thanks
    0
    Thanked 0 Times in 0 Posts
    thanks as the websites are very helpful. Again, I suppose since the FET is more difficult to calculate, chi-square is used but with statistical programs doing the "number crunching", it appears, at least to me, that FET should be used for most purposes. Is the FET even too time consuming for modern computer processing capabilities?

    My point being, why use an approximation (ie., chi-square) when you can get the exact answer (FET) regardless of sample size.

  9. #9
    R purist
    Points: 18,370, Level: 86
    Level completed: 4%, Points required for next Level: 480
    TheEcologist's Avatar
    Location
    The Netherlands.
    Posts
    1,590
    Thanks
    201
    Thanked 408 Times in 227 Posts
    Quote Originally Posted by helpwithstats View Post
    thanks as the websites are very helpful. Again, I suppose since the FET is more difficult to calculate, chi-square is used but with statistical programs doing the "number crunching", it appears, at least to me, that FET should be used for most purposes. Is the FET even too time consuming for modern computer processing capabilities?

    My point being, why use an approximation (ie., chi-square) when you can get the exact answer (FET) regardless of sample size.
    Point noted, However as I understand it the difference between the Chi-square and the FET becomes smaller as the expected cell count and table size grows. Therefore it doesn't really matter anyway.

    however at what size the tests become acceptably similar I dont know.

    Edit: There was actually a discussion on the R help list on this (not resolved):

    http://tolstoy.newcastle.edu.au/R/help/05/09/11961.html
    Last edited by TheEcologist; 08-22-2008 at 10:19 AM. Reason: Added R-help link
    The true ideals of great philosophies always seem to get lost somewhere along the road..

  10. #10
    Points: 5,591, Level: 48
    Level completed: 21%, Points required for next Level: 159

    Posts
    24
    Thanks
    0
    Thanked 0 Times in 0 Posts
    thanks for the helpful link. It appears this is debated topic among statisticians.

  11. #11
    Points: 1,929, Level: 26
    Level completed: 29%, Points required for next Level: 71

    Posts
    2
    Thanks
    0
    Thanked 0 Times in 0 Posts
    I've got a question related to this thread and I've been looking everywhere on the web but I can't find an answer.

    I know that if the assumptions (n<20, one of the cells < 5 [or a little bit less stringent maximal 20&#37;]) one can stick to Fisher's Exact Test.

    When should I use the exact version of the CHISQ (in SPSS)? Can it be used as an substitute for the FET (if so, i which cases)? In other words, is it equivalent?

    In 2x2 tables one will get both for the FET and CHISQ the 1-sided exact test in SPSS. Does the 1-sided CHISQ have the sample principle as the FET which uses upward diagonals and downward diagonals? Besides that for bigger tables one can use the 2-sided exact test for each only I found out. And does the exact test for CHISQ also assumes fixed margins (conditional) like the FET?

    Further I am thinking about if my data meets the assumptions of the FET, because I did an oberservational study and registered looking (left, right, not) in case of turning (left, right) as a driver and I registered looking (left, right,not) in combination with a bicyclist from (left, right, none) as a driver.

    See the first document at the bottom. In the case of the lady example with coffee and milk poured a new data collection would be the same since the lady must guess 48 of each (first or second milk) again and there are 48 cups of each (these are both know by forehand). Also, the document states that if one would do a recount or collecting new data and when those row or column marginals change then it's voilated. if only one marginal is fixed one can do a FET says the document.

    Does a constant row marginal in my study mean that I do for example 20 turning left and 40 turning right (row totals like in my first data collection) in a new data collection (i know/choose it by forehand) and observe looking behaviour (which probably is not the same). On the other hand, if I would have recorded those drivers on tape and score them again it ould result in the same 2x2 table with the same total column and row margins (this might be not a logical or allowed idea).


    This might be an interesting link:
    http://www.uvm.edu/~dhowell/StatPage...y%20Tables.pdf

    And (cast doubt on the relevance of marginals, did not read the article myself):
    http://www.sciencedirect.com/science...b7ad6e0fe61024

    Are there any other alternatives to CHISQ (for my problem, with 2x2 and 2x3 tables)?

    Is the Yates' correction a good alternative (I've read somewhere that it is very convervative)? I think it's called in SPSS 'Likelihood Ratio'. And maybe Barnard’s Test? It is only for 2x2 and not in SPSS.
    Last edited by matthijs0; 12-12-2009 at 01:22 PM.

  12. #12
    Points: 4,663, Level: 43
    Level completed: 57%, Points required for next Level: 87

    Posts
    118
    Thanks
    1
    Thanked 1 Time in 1 Post
    Kindly help me on the following.
    1. How to understand the result of Fisher's Exact Test? This test facility is available for free on certain websites. Is it a p-value or the value similar to Chisquare. For example, please see this.

    http://www.danielsoper.com/statcalc/calc29.aspx

    2. Are FET and Hypergeometric distribution one and the same? In Excel 2007, hypgeomdist function is available to find this out. How to punch data into it and understand the result?

  13. #13
    Dark Knight
    Points: 1,890, Level: 25
    Level completed: 90%, Points required for next Level: 10
    vinux's Avatar
    Posts
    1,880
    Thanks
    45
    Thanked 190 Times in 157 Posts
    My Answer is in Red.
    Quote Originally Posted by Dr.Appalayya View Post
    Kindly help me on the following.
    1. How to understand the result of Fisher's Exact Test? This test facility is available for free on certain websites. Is it a p-value or the value similar to Chisquare. For example, please see this.

    http://www.danielsoper.com/statcalc/calc29.aspx

    It is based on P value we take the decision. The test statistic is a probability here.


    2. Are FET and Hypergeometric distribution one and the same? In Excel 2007, hypgeomdist function is available to find this out. How to punch data into it and understand the result?

    In 2 x 2 FET , the test statistic is sum of hypergeometric probabilities. To calculate this in excel the 2 x 2 scenario... create all a ,b,c,d combinations such that a+b , a+c , b+c ,b+d are constant.
    Then calculate the probability.
    In the long run, we're all dead.

  14. #14
    Points: 4,663, Level: 43
    Level completed: 57%, Points required for next Level: 87

    Posts
    118
    Thanks
    1
    Thanked 1 Time in 1 Post

    FET/Chi-Square

    Quote Originally Posted by vinux View Post
    My Answer is in Red.
    I am sorry I don't understand how they are calculated on excel sheet. Can you please give a step-by-step method?

  15. #15
    Points: 1,929, Level: 26
    Level completed: 29%, Points required for next Level: 71

    Posts
    2
    Thanks
    0
    Thanked 0 Times in 0 Posts


+ Reply to Thread
Page 1 of 2 1 2 LastLast

           




Similar Threads

  1. Fisher's Exact Test
    By ReptileJK in forum Statistics
    Replies: 8
    Last Post: 03-26-2014, 07:32 AM
  2. chi square/Fisher's Exact and one tailed hypothesis?
    By Butterbean in forum Psychology Statistics
    Replies: 7
    Last Post: 01-04-2011, 03:29 PM
  3. Fisher's Exact Test?
    By purplehibiscus in forum Statistics
    Replies: 0
    Last Post: 07-17-2009, 09:07 AM
  4. Fisher's exact test
    By zeta09 in forum Biostatistics
    Replies: 0
    Last Post: 05-27-2009, 08:24 PM
  5. When to use Fisher's exact test
    By dfrisch in forum Statistics
    Replies: 1
    Last Post: 07-25-2008, 01:09 AM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts






Advertise on Talk Stats