Hi John,

Thanks for your interested in using beadarray.  If you could include the
output of the sessionInfo() command with your query it really helps, as
that gives lets everyone know the versions of the packages you're using.

The first error you've got seems to be in the splitting of the bead-level
text file.  This works by taking the two .locs files and tries to match
coordinate pairs from the txt file with one or the other of the two locs.
 Occasionally this code meets some weird situation that I haven't
encountered, and normally produces an (admittedly not very helpful) error
like the one you're seeing.

The second error sounds odder to me.  You should never get a single value
in record in the perBeadFile.txt files and the value 0.72 doesn't seem like
a BeadID, intensity or coordinate, which are the only values that
you'd expect in those files.  I would suspect it's either a corruption to
the file or something has been pasted in accidentally.

In both cases, if you'd like me to take a look at the offending files we
have an ftp site at:
ftp://ftp2.cancerresearchuk.org/pub/beadarray/

Just create a folder with your name and drop the files there.  However,
please bear in mind that the site is completely open and I can't easily
delete anything that is placed there, so if you'd rather put them somewhere
else that's fine to.

I hope that's some help,
Mike Smith

On Thu, Dec 8, 2011 at 12:18 PM, John Alexander <fbsja@leeds.ac.uk> wrote:

> Hi,
>   I must say that I'm fairly new to microarrays and is my first attempt.
> I have 2 chips with 6 heterozygous samples on one and wildtype
> on the other (poorly designed).The chip is MOUSEWG-6_V2.
>
> I have the raw data which is the output from iScan and needs to be
> processed
> using processSwathData function and also the Final data - which is the
> summarised data from GenomeStudio.  I have all the necessary files-
> Swath_Grn.locs,.tif,Metrics,_beadTypeFile.txt,perBeadTypeFile.txt for
> analysis.
>
> Running the processSwathData function with default values (I dont know how
> to
> find the value for swathOverlap parameter)
>
> processSwathData(inputDir = dir1, outputDir =dirOp1 , twoColour=NULL,
> textstring="_perBeadFile.txt", segmentHeight = 326, segmentWidth = 397,
> swathOverlap = 81, fullOutput = FALSE, newTextString=".txt", verbose =
> FALSE)
>
> Output...
> Ist chip:
> 5665095021_A_1
> 5665095021_A_2
> 5665095021_B_1
>
> Error in if (all(txt[txtDups[i + 1], 3:4] == txt[txtDups[i], 3:4])) { :
>  missing value where TRUE/FALSE needed
>
> 2nd Chip :
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>  :
>  scan() expected 'an integer', got '0.72'
>
> I noticed that in 5665095021_A_1_perBeadFile.txt, in line it has only one
> entry (0.72) instead of 4. Is there a way to bypass this problem because I
> cannot read into the function readIllumina()
>
>  On the other hand I am trying to proceed with the summarised Data
> from GenomeStudio. I donot have much information to perform analysis
>  on this output iScanb using beadarray.
> Is there a way to club the summarised data from both the chips.
>  I tried the combine function but it does not work.
>
> Any tutorials on this would be appreciated.
>
> Kind regards,
> John.
>
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>



-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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