[BioC] Agi4x44PreProcess

Francois Pepin fpepin at cs.mcgill.ca
Wed Dec 2 18:41:40 CET 2009

(Apologies, I had originally put BioC in bcc instead of cc, whoever is 
moderating the list should feel free to delete the original)

Dear Hemang,

Please use the bioconductor mailing list. This will allow other people
to help you in addition to ensuring that this e-mail will be archived
and searchable for other people who might have the same issue.

While I have commented on the usage of Agi4x44PreProcess and tried to
help people using it, I have never actually used it.

In this particular case, I would recommend that you read the help for
the function that you just used: ?read.AgilentFE.

I am 99% sure that your files were not "generated by the Agilent Feature
Extraction image analysis software", explaining why the function was
unable to read your files and giving you this error.

These files most likely originate from GEO. The GEOquery package will be
a lot more useful in your case.

You would then probably need to convert it into an RGList or a similar
object for the Agi4x44PreProcess package will be able to work.

I hope this helps,


On 12/02/2009 12:14 PM, Hemang Parikh wrote:
> Hi Francois,
> I found your e-mail address from Bioconductor mailing list. I am using
> Agi4x44PreProcess package. However, I am getting an error message while
> reading Agilent files with read.AgilentFE. I am just wondering if you
> can help me to resolve the issue.
> Thanks for your help,
> Hemang
> dd=read.AgilentFE(targets, makePLOT=FALSE)
> Read GSM187289.txt
> Read GSM187290.txt
> Read GSM187291.txt
> Read GSM187292.txt
>   INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord
> Error in read.AgilentFE(targets, makePLOT = FALSE) :
>     the script will stop now

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