R devel - Aug 2003 - scan file error (PR#3738)

Full_Name: Bart
Version: 1.7.1
OS: XP
Submission from: (NULL) (150.203.41.62)


When trying to load microarray slides (gpr format) into R 1.7.1, I get the
following error message

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :

        line 1057 did not have 43 elements

I have been able to load the files on another computer before including an XP
machine. I have also tried to load a different set of gpr files, that also
worked on an earlier version, but still get the same error message.
Using an earlier version of R (1.3.1)I did not have these problems.
Does anyone know of compatibilty issues between R 1.7.1 and Windows XP?

Thanks,

Bart

On Wed, 13 Aug 2003 04:07:27 +0200 (MET DST), you wrote:
>Full_Name: Bart
>Version: 1.7.1
>OS: XP
>Submission from: (NULL) (150.203.41.62)
>
>
>When trying to load microarray slides (gpr format) into R 1.7.1, I get the
>following error message
>
>Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
:
>
>        line 1057 did not have 43 elements
>
>I have been able to load the files on another computer before including an
XP
>machine. I have also tried to load a different set of gpr files, that also
>worked on an earlier version, but still get the same error message.
>Using an earlier version of R (1.3.1)I did not have these problems.
>Does anyone know of compatibilty issues between R 1.7.1 and Windows XP?
What does line 1057 look like?  What did your command look like that
tried to read the file?  

Please read ?bug.report and give us the necessary information that we
can use to reproduce your problem.  If it really is a bug, we won't be
able to fix it without that.  However, chances are that in simplifying
this to an example you can post, you'll find that it's really not a
bug.

Duncan Murdoch

Having dealt quite a bit with different versions of GenePix Data Results
files (GPR) on different systems (including WinXP Pro w/ R v1.7.1) my
guess is that your GPR file has single qoutation marks in the Name or the
ID columns. Typical is "3' end bla bla" etc.

If I remember correctly, I've seen exactly that error message because of
this and it can be dealt with by using the correct 'quote' argument. Try
quote="" instead of the the default one. Sorry for not being able to
be
more direct, but my laptop is on service and I do not have time to go to
the backup archives to find the details. 

I do not know of any difference between R v1.7.1 and previous versions. If
you still can't get it to work, you can test to read your GPR file with
the com.braju.sma package, which has been able read all GPR versions
this far (except from an unrelated problem reported with GPR v1.5 I've got
this week). See http://www.maths.lth.se/help/R/com.braju.sma/ for install
and read instructions. If you get errors I could take a look at the file,
because I doubt it is a R bug.

Best wishes

Henrik Bengtsson

Dept. of Mathematical Statistics @ Centre for Mathematical Sciences 
Lund Institute of Technology/Lund University, Sweden (+2h UTC)
+46 46 2229611 (off), +46 708 909208 (cell), +46 46 2224623 (fax)
h b @ m a t h s . l t h . s e, http://www.maths.lth.se/~hb/

On Wed, 13 Aug 2003 bart.rossel@anu.edu.au wrote:
> Full_Name: Bart
> Version: 1.7.1
> OS: XP
> Submission from: (NULL) (150.203.41.62)
> 
> 
> When trying to load microarray slides (gpr format) into R 1.7.1, I get the
> following error message
> 
> Error in scan(file = file, what = what, sep = sep, quote = quote, dec =
dec,  :
> 
>         line 1057 did not have 43 elements
> 
> I have been able to load the files on another computer before including an
XP
> machine. I have also tried to load a different set of gpr files, that also
> worked on an earlier version, but still get the same error message.
> Using an earlier version of R (1.3.1)I did not have these problems.
> Does anyone know of compatibilty issues between R 1.7.1 and Windows XP?
> 
> Thanks,
> 
> Bart
> 
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