[BioC] li.wong vs fit.li.wong

Tibor van Rooij Tibor van Rooij" <tibor@cs.mcgill.ca
Thu, 26 Sep 2002 14:49:37 -0400


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Hi! do li.wong( ) and fit.li.wong( ) have their matrix indeces reversed?

when I use the example:

x <- sweep(matrix(2^rnorm(600),30,20),1,seq(1,2,len=3D30),FUN=3D"+")

and I use li.wong(x,verbose=3DT)

it claims it has :

chips used=3D 20 , probes used=3D 30

however when I use fit.li.wong(x,verbose=3DT)

it says it has:

chips used=3D 30 , probes used=3D 20

Does anybody know why? What I really would like to do is give it a =
matrix and get a matrix with of the same dimension with the normalized =
values back as I can with normalize.quantiles(x) for quantile =
normalization.

Has anybody succeeded in doing this?

Tibor
_______________________________=20
Tibor van Rooij=20
Bioinformatician=20
Montreal Genome Centre
McGill University, Duff Building=20
Tel:  (514) 398-2497
Fax: (514) 398-1838


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<DIV><FONT face=3DArial size=3D2>Hi! do li.wong( ) and fit.li.wong( ) =
have their=20
matrix indeces reversed?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>when I use the example:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>x &lt;-=20
sweep(matrix(2^rnorm(600),30,20),1,seq(1,2,len=3D30),FUN=3D"+")</FONT></D=
IV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>and I use =
li.wong(x,verbose=3DT)</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>it claims it has :</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>chips used=3D 20 , probes used=3D =
30</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>however when I use=20
fit.li.wong(x,verbose=3DT)</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>it says it has:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>chips used=3D 30 , probes used=3D =
20</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Does anybody know why? What I really =
would like to=20
do is give it&nbsp;a matrix and get a matrix with&nbsp;of the same =
dimension=20
with&nbsp;the normalized values back as I can with =
normalize.quantiles(x) for=20
quantile normalization.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Has anybody succeeded in doing =
this?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Tibor</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>_______________________________ =
<BR>Tibor van Rooij=20
<BR>Bioinformatician <BR>Montreal Genome Centre<BR>McGill University, =
Duff=20
Building <BR>Tel:&nbsp; (514) 398-2497<BR>Fax: (514) =
398-1838</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></BODY></HTML>

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