[BioC] read.GenePix not opening connection

[Paquet, Agnes]

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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