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The following is the matrix which I am using for finding differentially expressed genes using the multtest package.

ID_REF     GSM362168 GSM362169 GSM362170 GSM362171 GSM362172 GSM362173 GSM362174      
244901_at   5.171072  5.207896  5.191145  5.067809  5.010239  5.556884  4.879528      
244902_at   5.296012  5.460796  5.419633  5.440318  5.234789  7.567894  6.908795

the code that I used is

cl<-c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
      0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
      1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
stat <- mt.teststat(conthyp,classlabel=cl,test="t.equalvar")

where conthyp is the matic and cl is the classlabel. I get the following error

Error: C stack usage is too close to the limit

I am not sure where I am making the mistake.

Zheyuan Li
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Stacey John
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    If you made a [reproducible example](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) that demonstrates your question / problem, we would find it easier to answer. – Andrie Aug 30 '12 at 08:39
  • Shouldn't your `classlabel` argument have as many entries as the number of columns in `conthyp`? – seancarmody Aug 30 '12 at 10:08
  • yes i have only given a portion of the matrix here whereas the original one contains 79 columns excluding the first(gene-id). – Stacey John Aug 30 '12 at 12:09
  • The error indicates that the code is likely going into infinite recursion. Can you post your `conthyp` with `dput(conthyp)`? It will make it easy for us to cut and paste into our R sessions. It would actually be better if you tried to see if the problem occurred on a smaller matrix, and posted that smaller matrix instead. – nograpes Aug 30 '12 at 14:36
  • I do not understand how do I have to do it using the dput??? – Stacey John Aug 31 '12 at 08:19

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