[BioC] Importing SMD data

[Jeremy Gollub]

Hi, Georgia -

At a guess, your .xls file from SMD is in an old format.  The current
version of read.SMD expects column headers such as "Ch1 Intensity
(Median)."  If you instead have headers like "CH1I_MEDIAN," I don't
think read.SMD will handle it.

If this is the case, you should be able to use read.maimages() from the
limma package, with source="smd.old".  You could then use the convert
package from BioConductor to make appropriate marray objects from the
limma object(s).

Hope this helps -

--
Jeremy Gollub, Ph.D.
jgollub at genome.stanford.edu
(W) 650/736-0075

On Tue, 6 Sep 2005, Georgia Chan wrote:

> Hi all,
>  I am a newbie to R and BioConductor and
>  (at the moment :) have trouble importing
>  SMD data to R, using read.SMD/read.SMD2
>  
>  In the working directory, I have 2 files:
>  "14037.xls" with data for one array and
>  its corresponding GAL file "14037.gal",
>  produced by SMD.
>  
>  Below is the debug info from R.
>  
>  Mant thanks in advance,
>  georgia
>  
>  
>  ----------------------------------------------
>  Output:
>  ----------------------------------------------
>  > fnames
>  [1] "14037.xls"
>  
>  > read.SMD(fnames=fnames, path=path, DEBUG=TRUE)
>  [1] "14037.xls"
>  Generating layout from 14037.xls
>  [1] "Reading Gal file"
>  Error in "[.data.frame"(dat, , info.id) : undefined columns selected
>  
>  > read.SMD2(fnames=fnames, DEBUG=TRUE)
>  Generating layout from 14037.xls
>  Error in if (skip > 0) readLines(file, skip) :
>          missing value where TRUE/FALSE needed
>  
>  > readLines("14037.gal",30)
>   [1] "ATF\t1.0"
>   [2] "20\t5"
>   [3] "\"Type=GenePix ArrayList V1.0\""
>   [4] "\"BlockCount=16\""
>   [5] "\"BlockType=0\""
>   [6] "\"Block1= 400, 400, 100, 19, 225, 19, 225\""
>   [7] "\"Block2= 4896, 400, 100, 19, 225, 19, 225\""
>   [8] "\"Block3= 9392, 400, 100, 19, 225, 19, 225\""
>   [9] "\"Block4= 13888, 400, 100, 19, 225, 19, 225\""
>   [10] "\"Block5= 400, 4896, 100, 19, 225, 19, 225\""
>   [11] "\"Block6= 4896, 4896, 100, 19, 225, 19, 225\""
>   [12] "\"Block7= 9392, 4896, 100, 19, 225, 19, 225\""
>   [13] "\"Block8= 13888, 4896, 100, 19, 225, 19, 225\""
>   [14] "\"Block9= 400, 9392, 100, 19, 225, 19, 225\""
>   [15] "\"Block10= 4896, 9392, 100, 19, 225, 19, 225\""
> 
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