[BioC] problem reading genepix files using both marray andlimma functions

[michael watson (IAH-C)]

Ditto.  I'd be happy to look over a couple of your gpr files.

I have had problems with gpr files before, but have often tracked the
problem down to the user:

1) had opened the files in excel and then saved as tab-delimited text
2) had (somehow) put a carriage return in the middle of a line
3) had manually edited some of the gene names in only some of the files
(DOH!)
Etc
Etc

Things would be a lot easier if us bioinformaticians didn't have "users"
;-)

Mick

-----Original Message-----
From: Gordon Smyth [mailto:smyth at wehi.edu.au] 
Sent: 17 August 2004 00:12
To: Bela Tiwari
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] problem reading genepix files using both marray
andlimma functions


The first things to try are

1. Upgrade to the latest version of limma from
http://bioinf.wehi.edu.au/limma 2. Check with your associate that the
genepix gpr files really have not 
been edited. Emphasise that you really need files as they are straight
out 
of GenePix.

You should also tell us what versions of R and the packages you are
using, 
type:
version
packageDescription("limma")
and include the output in an email.

If you take both steps above and still have a problem, then you can send
me 
a couple of your gpr files. The gpr files should be in a zip or similar 
file to prevent any further conversions by the mailer.

Gordon

At 01:37 AM 17/08/2004, Bela Tiwari wrote:
>Hello,
>
>
>Last week I was sent GenePix data files from an associate. As far as 
>I'm aware, these files have not been edited in any way before being 
>sent to me.
>
>My aim was to load them up and run some marray and/or limma functions 
>on the data.
>
>First I tried to load the files (16 of them) using read.GenePix(), but 
>this failed with an error:
>
>    Error in "colnames<-"( `*tmp*`, value = fnames) :
>                length of dimnames [2] not equal to array extent
>
>
>Then I tried loading a file individually using read.GenePix() and that 
>worked fine, however, subsets of files did not.
>
>I then read through some of the relevant Bioconductor mailing list 
>posts that I could find, and decided to try the read.maimages function 
>as an alternative.
>
>This I did, only to get errors such as:
>
>       line 35162 did not have 43 elements
>
>
>So, I tried loading the files individually, using read.maimages() to 
>see if I could track down the "problem" files, and then look at them to

>see if there was an issue with certain lines within those files.
>
>I did this, and found that 5 of my 16 files would not load using 
>read.maimages and gave errors like the one directly above.
>
>One file  gave a different error:
>
>    "number of items read is not a multiple of the number of columns"
>
>giving me a total of 6 out of 16 files that won't load using 
>read.maimages.
>
>Tackling the latter error first - I looked at the file, and saw an 
>incomplete line at the bottom of the file. I got rid of that, and tried

>to load the file using read.GenePix(). I still received a warning 
>message about the fact that the number of items read is not a multiple 
>of the number of columns.  I cannot spot the problem in the edited 
>version of the file. The edited file does, however, now read in without

>error using read.maimages().
>
>
>I then tried loading the files that "failed" with the first error 
>message above individually with read.GenePix() and this works.
>
>I did look at some of the files to try and see what the problem was 
>(ie. whether there was anything obviously strange at the lines 
>indicated as problems by the read.maimages error message), but I can't 
>see anything.
>
>
>I then took the "successful" subset of my files ( those I could read in

>as individual files using read.maimages), and tried to read those in as

>a group. This didn't work either, but the error I got was:
>
>Error in "[.data.frame"(obj, , columns$Rf) :
>                   undefined columns selected
>
>So, I specified the columns explicitly in the read.maimages command, 
>but I still got the same error.
>
>
>Thankfully, a recent posting to the mailing list
>(http://files.protsuggest.org/biocond/html/3512.html)  mentioned issues

>related to this, and Dave Nelson gave a solution that could be 
>implemented. I did this, and my "successful" files then read in just 
>fine using this hacked version of read.maimages().
>
>I also tried using the read.Genepix() function to read in just the 
>group of "successful" files and that gives the error:
>
>        Error in "colnames<-"( `*tmp*`, value = fnames) :
>                length of dimnames [2] not equal to array extent
>
>
>So, overall, my questions are:
>
>Is there anyone out there who would be willing to scan over one of my 
>"successful" files and one of my "failed" files and see if they can 
>spot the problem? The errors suggest that the problem should be easy to

>spot...but I can't see it. Even with all the gymnastics related above, 
>I still have a situation where I have only managed to load about half 
>of the files I have.
>
>Is there anyone else who has had these experiences of groups of GenePix

>files being so seemingly inconsistent as far as being able to read them

>using Bioconductor functions?  And if so, do you have any advice on how

>too make life as easy as possible?
>
>Does anyone have any other comments about the internal 
>workings/assumptions of functions such as read.maimages in comparison 
>to, say, functions like read.GenePix, and which may be more forgiving, 
>or have known issues, etc?
>
>
>Sorry this is such a long mail!
>
>
>best wishes,
>
>Bela Tiwari
>
>*************************
>Dr. Bela Tiwari
>Lead Bioinformatician
>
>CEH Oxford
>Mansfield Road
>Oxford, OX1 3SR
>01865 281975

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