[BioC] (no subject)

[Laurent Gautier]

On Thu, May 15, 2003 at 06:31:07PM +0530, rinku saha wrote:
> 
> 
> 
> 1)I installed R-1.7.0  in Sgi machine(irix6.5).I installed all the
> >> bioconductor packages too.
> >> After that i did put all my >cel files under one directory and then move
> >> into that directory and Start  R.Then i gave library(affy) to load it.
> >> Welcome to Bioconductor
> >>   To view some introductory material.........
> >>    Simply type.......
> >>   Creating a new  generic function for "summary" in package
> >> Biobase
> >> {1} TRUE
> >>
> >> My question is did it reall yy load the package affy.
> >>
> >> 2)When  i write data <-ReadAffy()
> >> it gives these:
> >>
> >> 1: the condition has length > 1 and only the first element will be used 
> >in:
> >> if (dim(intensity(cel)) != dim.intensity) stop(paste("CEL file dimension
> >> mismatch !\n(file",













those are 'warnings'. They do not cause harm. Your data were loaded.
I would suggest you try the devel version.
(note: "data" is an helpful function in R. Try to find an another name
for your variable)

Hopin' it helps,

L.


> >>
> >> My question is how can i make it work to read my .cel file.
> >> I am sending you an example .cel file
> >> [CEL]
> >> Version=3
> >>
> >> [HEADER]
> >> Cols=536
> >> Rows=536
> >> TotalX=536
> >> TotalY=536
> >> OffsetX=0
> >> OffsetY=0
> >> GridCornerUL=237 234
> >> GridCornerUR=4492 243
> >> GridCornerLR=4490 4508
> >> GridCornerLL=235 4499
> >> Axis-invertX=0
> >> AxisInvertY=0
> >> swapXY=0
> >> DatHeader=[73..46225]  MG2000062256AA:CLS=4733 RWS=4733 XIN=3  YIN=3  
> >VE=17
> >>        2.0 06/22/ 0 11:15:55      GridVerify=Success   Hu6800.1sq
> >>                 6
> >> Algorithm=Percentile
> >> 
> >AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004
> >>
> >> [INTENSITY]
> >> NumberCells=287296
> >> CellHeader=X	Y	MEAN	STDV	NPIXELS
> >>   0	  0	1447.3	294.2	 36
> >>   1	  0	34282.8	4017.5	 36
> >>   2	  0	1528.0	244.9	 36
> >>   3	  0	33889.3	4679.7	 36
> >>   4	  0	1073.5	211.4	 36
> >>   5	  0	1493.8	235.2	 36
> >>   6	  0	26558.8	5903.9	 36
> >>   7	  0	1557.5	259.3	 36
> >>   8	  0	25951.8	3178.6	 30
> >>   9	  0	1497.0	292.3	 36
> >> 10	  0	26122.8	3989.7	 36
> >> 11	  0	1577.3	271.9	 36
> >> 12	  0	25029.8	4386.5	 36
> >> 13	  0	1454.8	229.0	 36
> >> 14	  0	25128.5	5666.1	 36
> >> 15	  0	1602.0	242.9	 36
> >> 16	  0	26180.0	6859.9	 36
> >> 17	  0	1652.8	304.7	 36
> >> 18	  0	26311.8	7985.2	 36
> >> 19	  0	1655.0	295.9	 36
> >> 20
> >>
> >>
> >>
> >> 3)when i try to load tcl/tk  it says:
> >> Loading required package: tcltk
> >> Error in firstlib(which.lib.loc, package) :
> >>         Tcl/Tk support is not available on this syError: syntax error
> >> Please do help me out.
> >>
> >> Thanks
> >> RInku
> >>
> >> _________________________________________________________________
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> >> Switch to Hallmark channel.
> >>
> >> ______________________________________________
> >> R-help at stat.math.ethz.ch mailing list
> >> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> >>
> >
> >
> 
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-- 
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currently at the National Yang-Ming University in Taipei, Taiwan
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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent