Fwd: Re: Fwd: Re: [BioC] Heatmap function

[Marcus]

>Hello again... I still have some questions. If you have the time Sean (or 
>someone else) I would be very grateful.
>
>Yes, the M-values are log, but I have checked and I do not have any 
>infinite or NaN values in the matrix.
>
>I have som questions regarding hclust. It says that the function 
>calculates the distances row-wise in the helpfile. But what I do not 
>understand is that I have chips with M-values that are seperated 
>column-wise. Am I supposed to have them by row instead?
>
>Another question.
>The function looks like this hclust(as.dist(myobject),  method ="complete")
>The as.dist have euclidean distance by default and the hclust have 
>"complete" as default. What does that mean, that It calculates two?? 
>distances or that on distancemeasure is "shut off"?
>
>And the final question.
>If I use hclust to create an object to use in the heatmap function, is 
>that the object that I give to the heatmapfunction both as colv and rowv?
>heatmap(x=mymatrixwithcorrelations, Rowv = 
>distanceofmymatrixwithcorrelations, 
>Colv=distanceofmymatrixwithcorrelations, distfun=dist, hclustfun = hclust 
>... etc) ?
>
>Or is there a way to fist cluster by row in hclust and then by column?
>
>Thanks for the help
>
>/ A very confused person
>
>
>
>
>>>I assume that the M values are a log, so you might check to be sure that you
>>>do not have infinite or NaN results from taking logs of zero and the like.
>>>
>>>As for dist, use ?dist to get the help file for dist.  There are other
>>>distances that you can use (by changing the arguments to dist).  However,
>>>one trick that I have found useful is to do your clustering as you want it
>>>done before calling heatmap and then call heatmap with Rowv=rowclust and
>>>Colv=colclust where rowclust and colclust are "cluster" objects that you can
>>>obtain from calling hclust.  In this way, you can make your clusters "look
>>>good" before spending the time having heatmap do it for you each time.
>>>
>>>Hope that helps.  Oh, by the way, I am absolutely not an expert, so check
>>>with other folks, also.
>>>
>>>Sean
>>******************************************************************************************* 
>>

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Marcus Gry Björklund

Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
Department of Molecular Biotechnology
106 91 Stockholm, Sweden

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