[BioC] Reading data from SMD database

Aedin aedin.culhane at ucd.ie
Tue Feb 24 17:50:43 MET 2004

Thanks a million Colin,
I will try this thanks.

-----Original Message-----
From: Colin Smith [mailto:colin at colinsmith.org]
Sent: 24 February 2004 16:47
To: Aedin
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Reading data from SMD database


I played around with SMD import last summer and created a function that 
much more intelligently imports data from the SMD. The interesting 
thing about the "Excel" files you get from the SMD is that they aren't 
actually Excel files. Instead, they are just text files. R can read 
them just fine.

I unfortunately never got around to adding the function into 
marrayInput. I haven't tested it since last summer so either the SMD or 
marrayInput schemas may have changed a bit. I'd be happy to help you 
debug/fix it if incompatibilities have crept in. You can download it 


It tries to shoehorn as much information from the raw data files as 
possible into the marray classes. The only thing it doesn't import is 
the control spots because the SMD doesn't include that information in 
their raw data files. The input is just a character vector of file 
names. The files should have all used the same chip layout.


On Feb 24, 2004, at 7:59, Aedin wrote:

> Date: Tue, 24 Feb 2004 13:58:45 +0000
> From: Aedin <aedin.culhane at ucd.ie>
> Subject: [BioC] Reading data from SMD database
> To: bioconductor at stat.math.ethz.ch
> Hi all,
> Whats the easiest way to read published data in the SMD database into 
> R.
> The "raw data" from smd.stanford.edu seems to download as multiple 
> excel
> files, which fail to be read into R if I use read.SMD().  Am I 
> downloading
> the incorrect format file from SMD?
> Thanks so much for any help,
> Aedin

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