Hi,

I am using the "processSwathData" command from the beadarray package to
process Illumina iScan files and I am getting the following error:

processSwathData("./3999538058", outputDir="./3999538058", twoColour=NULL, textstring="_perBeadFile.txt", segmentHeight=326, segmentWidth=397, fullOutput=T, newTextString=".txt")

Error in unlist(scan(file, sep = sep, what = list(integer(), integer(),  :
  error in evaluating the argument 'x' in selecting a method for function
'unlist': Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings,  :
  scan() expected 'a real', got '8880.3552.084'

Any idea? Any help would be greatly appreciated.

Here is the sessionInfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8   
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8  
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods 
[8] base    

other attached packages:
[1] beadarray_2.14.1    ggplot2_1.0.1       Biobase_2.24.0    
[4] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.1 base64_1.1           BeadDataPackR_1.16.0
 [4] colorspace_1.2-6     DBI_0.3.1            digest_0.6.8       
 [7] GenomeInfoDb_1.0.2   GenomicRanges_1.16.4 grid_3.1.1         
[10] gtable_0.1.2         illuminaio_0.6.1     IRanges_1.22.10    
[13] limma_3.20.9         MASS_7.3-39          munsell_0.4.2      
[16] plyr_1.8.1           proto_0.3-10         Rcpp_0.11.5        
[19] reshape2_1.4.1       RSQLite_1.0.0        scales_0.2.4       
[22] stats4_3.1.1         stringr_0.6.2        XVector_0.4.0      

Thanks,
Harpreet

Hi Mike,

Many thanks for your prompt reply.

the "_perBeadFile.Txt" is here,

https://www.dropbox.com/sh/he86j5wjdwrsrny/AAD_BVBNnWXo23foCHFzlW9Ba?dl=0

Let me know if there is any problem in accessing the file.

Thanks,

Harpreet

Hi Harpreet,

The problem seems to be with line 969239 in "3999538058_H_perBeadFile.txt".  For some reason the fourth column contains the entry 8880.3552.084, which is clearly not a coordinate.  The simplest fix is to manually edit that entry to be 8880.355 (there's almost always 7 sig. fig.  in those columns).  The file can then be read normally.

However, you might want to do some more digging.  There's a blank entry at line 969342 and the very final line of the file ends abruptly.  It looks to me like several thousand lines have been cut out and pasted into the end of the file.  If you have another copy of the file somewhere you might want to check that there hasn't been some corruption introduced in copying it between devices.  

Mike