[BioC] read.GenePix not opening connection

[Amy Mikhail]

Hi Agnes,

Amazing! It worked! Thank you so much.

Now, do I just repeat the same thing for the other 5 files?

Thanks again,
Amy.


---------------------------------------------------------------------------
> Hi Amy,
>
> Did you switch your working directory to the directory containing your
> gpr files? By default, read.GenePix() is looking for fnames in ".". To
> switch directory, you can either do:
>
> datadir <- system.file("Samsfish", package = "marray")
> setwd(datadir)
> data <- read.GenePix(fnames="samcellINF11a.gpr")
>
> or
>
> data <- read.GenePix(fnames="samcellINF11a.gpr", path=datadir)
>
> I hope this will help,
>
> Agnes
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail
> Sent: Wednesday, June 29, 2005 1:22 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] read.GenePix not opening connection
>
> Hi,
>
> Unfortunately there are more error messages;
>
>> data <- read.GenePix(fnames=SamsfishTargets$FileName)
> Error in file(con, "r") : unable to open connection
> In addition: Warning message:
> cannot open file './NA'
>
> and for the next one...
>
>> data <- read.GenePix(fnames="samcellINF11a.gpr")
> Error in file(con, "r") : unable to open connection
> In addition: Warning message:
> cannot open file './samcellINF11a.gpr'
>
> Cheers,
> Amy.
>
> P.s., just a thought but when I had a look in the .gpr files with
> notepad
> they specified the path for the gal file as:
>
> ATF	1.0
> 29	56
> "Type=GenePix Results 3"
> "DateTime=2005/05/09 09:18:06"
> "Settings="
> "GalFile=D:\My Documents\sam\salmonid seq database\Grasp
> arrays\16kGAL_txt.gal"
>
> ...which is where it is stored on the GenePix computer, not the one I'm
> currently working from...
>
> Could this be the problem?
>
>
> ------------------------------------------------------------------------
> ---
>> Hmmm.  I have never *just* used the targets argument.
>>
>> What happens when you try:
>>
>> data <- read.GenePix(fnames=SamsfishTargets$FileName)
>>
>> or
>>
>> data <- read.GenePix(fnames="samcellINF11a.gpr")
>>
>> ??
>>
>>
>>
>> -----Original Message-----
>> From:	bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail
>> Sent:	Wed 29/06/2005 8:51 PM
>> To:	bioconductor at stat.math.ethz.ch
>> Cc:
>> Subject:	Re: [BioC] read.GenePix not opening connection
>>
>> Hi,
>>
>> Code is below:
>>
>>> library(marray)
>>> dir(system.file("Samsfish", package = "marray"))
>> [1] "16kGAL.gal"        "fishData.txt"      "samcellINF10b.gpr"
>> [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr"
>> [7] "samcellINF8a.gpr"  "samcellINF9a.gpr"
>>> datadir <- system.file("Samsfish", package = "marray")
>>> SamsfishTargets <- read.marrayInfo(file.path(datadir,
> "fishData.txt"))
>> data <- read.GenePix(targets=SamsfishTargets)
>> Error in file(con, "r") : unable to open connection
>> In addition: Warning message:
>> cannot open file './samcellINF8a.gpr'
>>> ?read.GenePix
>>> data <- read.GenePix(targets=SamsfishTargets)
>> Error in file(con, "r") : unable to open connection
>> In addition: Warning message:
>> cannot open file './samcellINF8a.gpr'
>>
>> The contents of fishData.txt reads:
>>
>> 	fileName	slideNumber
>> 1	samcellINF7a.gpr	1
>> 2	samcellINF8a.gpr	2
>> 3	samcellINF9a.gpr	3
>> 4	samcellINF10b.gpr	4
>> 5	samcellINF11a.gpr	5
>> 6	samcellINF12a.gpr	6
>>
>> (spaces are tabs).
>>
>> So, what have I done wrong?
>>
>> Cheers,
>> Amy.
>>
>>
> ------------------------------------------------------------------------
> ---
>>> Please post all your code, including the contents of whatever file
> you
>> read into SamsfishTargets.
>>>
>>> The error you are getting is because R cannot find the files you are
>> telling it to open.  99.999999999% of the time this is user error :-)
>>>
>>> Mick
>>>
>>>
>>>
>>> -----Original Message-----
>>> From:	bioconductor-bounces at stat.math.ethz.ch on behalf of Amy
> Mikhail
>> Sent:	Wed 29/06/2005 8:34 PM
>>> To:	bioconductor at stat.math.ethz.ch
>>> Cc:
>>> Subject:	[BioC] read.GenePix not opening connection
>>>
>>> Hi,
>>>
>>> I am new to microarray analysis and have been trying to use marray
> (in R
>> 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't
>> worked...
>>>
>>> There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample
>> description .txt file and a .gal file in my directory (folder
> containing
>> files is called Samsfish).  I've been trying to copy the example in
> the
>> vignette entittled "Quick Start Guide for marray".  It worked fine up
>> until the following line of code:
>>>
>>>> data <- read.GenePix(targets=SamsfishTargets)
>>>
>>> ...which gives me this error message:
>>>
>>> Error in file(con, "r") : unable to open connection
>>> In addition: Warning message:
>>> cannot open file './samcellINF8a.gpr'
>>>
>>> (or variations on a theme)
>>>
>>> Do you know what this means?
>>>
>>> What can I do about it?
>>>
>>> Many thanks,
>>> Amy
>>>
>>>
>>>
>>> -------------------------------------------
>>> Amy Mikhail
>>> Research student
>>> University of Aberdeen
>>> Zoology Building
>>> Tillydrone Avenue
>>> Aberdeen AB24 2TZ
>>> Scotland
>>> Email: a.mikhail at abdn.ac.uk
>>> Phone: 00-44-1224-272880 (lab)
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>
>>>
>>>
>>>
>>
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>>
>>
>>
>
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