[BioC] Affy High Throughput arrays

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Fri Jun 29 04:17:09 CEST 2007

On Jun 28, 2007, at 7:06 PM, ssls sddd wrote:

> Dear list,
> I am using gcrma to analyze a bunch of Affy arrays and have the  
> following
> error:
> Computing affinities[1] "Checking to see if your internet  
> connection works..."
> [1] "Environment hthgu133acdf was not found in the Bioconductor  
> repository."
> [1] "Checking to see if your internet connection works..."
> [1] "Environment hthgu133aprobe was not found in the Bioconductor  
> repository."
> Error in get(x, envir, mode, inherits) : variable "hthgu133aprobe"  
> was not found
> I happened to search the archive and found the very similar question
> Sanchita had almost a year ago but I did not find any clue related  
> to this.
> I appreciate any help on this.

Alex, first let me quote from Thomas reply to you recently

If you post a message on a new topic to this list, then please start a
new email thread instead of replying to an old thread that deals with a
different topic."

For those of us who use a reasonable email reader, we can see the  
different discussions in threads. It is slightly irritating that you  
do not start a new thread.

Anyway, the error comes from the fact that you need a probe package  
in order to run GCRMA and appearently no-one has supplied that  
package to Bioconductor.

It seems as if the high throughput array may have special issues,  
which I don't know anything about.


> Sincerely,
> Alex
> 	[[alternative HTML version deleted]]
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