[BioC] Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,

Sally sagoldes at shaw.ca
Tue Jan 22 04:54:48 CET 2008


THANK YOU SO MUCH!!!!! AND THANK YOU FOR REPLYING SO QUICKLY!!!

Sally
----- Original Message ----- 
From: "Henrik Bengtsson" <hb at stat.berkeley.edu>
To: "Sally" <sagoldes at shaw.ca>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Monday, January 21, 2008 6:52 PM
Subject: Re: [BioC] Error in scan(file, what, nmax, sep, dec, quote, skip, 
nlines, na.strings,


> On Jan 21, 2008 5:24 PM, Sally <sagoldes at shaw.ca> wrote:
>> I am using limma and am trying to set up an ExpressionSet.  When I use 
>> the following script to read in a table  of expression data (17,329 rows 
>> x 29 columns, tab delimited):
>>
>> exprdata<-read.table("exprsData.txt", header=TRUE)
>
> If it is a tab-delimited file, it is safer it you specify that
> explicitly, i.e. use argument sep="\t".  The default recognizes any
> white space, e.g. if you have a "feature" with a space in the name it
> will not work.
>
>>
>> I get the following error message:
>>
>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, 
>> na.strings,  :
>>   line 304 did not have 29 elements
>>
>>
>>
>> I looked at line 304 and it looks fine.  All 29 columns have data.
>
> Typically the error messages are useful, so treat it as if there
> indeed is a problem on that line.  There might be empty spaces/tabs
> etc at the end of that line.  See ?read.table for options.  See
> especially arguments 'strip.white', 'fill', and 'comment.char'.
>
> Also, try to read data from the first 303 rows using argument
> nrow=303.  Do you get what you expect?
>
>>
>> I have also set options(expressions=400000)
>>
>> Have I reached some maximum # of expressions that can be read in, or is 
>> it another problem?  If I have reached a maximum #, is there a fix?
>
> That option has nothing to do with gene expression data.  It deals
> with syntactical R expression (think programming language).
>
> /Henrik
>
>>
>>
>> My exprsData.txt file looks like this (note this is not the whole 
>> spreadsheet)
>>
>>       Feature c0M1 c0M2 c0M3 c0M4
>>       U179971 -4.7472 -4.43814 -4.3977 -2.97843
>>       e1 -0.24565 -0.53124 0.109064 -0.01936
>>       e2 -0.71906 0.035403 -0.16786 0.528748
>>       e3 -0.17362 0.32998 -0.0791 -0.50046
>>       e4 0.065989 0.003221 -0.30596 -0.42857
>>       e5 0.269098 -0.34523 -0.98694 -0.57842
>>       e6 0.038301 -0.09612 0.190023 -0.10283
>>       e7 -0.06462 -0.56698 -0.34373 0.285194
>>       e8 -1.10146 -0.06621 0.337491 -0.1891
>>       CA054869 -0.83861 0.145514 -0.40484 -0.18785
>>       CB490276 -0.71377 0.569419 -0.99984 -0.51384
>>
>>
>> Thank you
>>
>> Sally Goldes
>>         [[alternative HTML version deleted]]
>>
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>
>
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