[BioC] read.GenePix not opening connection

Paquet, Agnes apaquet at medsfgh.ucsf.edu
Wed Jun 29 22:55:57 CEST 2005


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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