Just to confirm what's been said before, the code to read the image files is
specifically written to read 16bit TIFF's.  It may well be that the
conversion from jpeg to tiff creates an 8 bit tiff (I can't remember the
defaults in Photoshop) and this would well and truly break the results.
That said I'd be surprised if it ran at all, as I would anticipate a
segmentation fault if it tries to read data this isn't actually in the
image.

Mike Smith

On 7/26/07, Krys Kelly <kak28@cam.ac.uk> wrote:
>
>
> I am having a problem with bead level data.
>
> I have .txt files containing over 900,000 lines with four columns: Code,
> Grn, GrnX and GrnY.
>
> The image files are .jpg rather than .tif. I have converted the .jpg
> images
> to .tif using Adobe Photoshop (trying several of the conversion options).
> They always look like a beautiful starry night sky, which I think is what
> is
> expected.
>
> However, the data in the beadarray object is not what I expected.  In G
> there are a lot of negative and zero values and all the Gb values are
> zero.
>
> On Wednesday, I downloaded the latest version of R, beadarray and the
> packages it depends on (see sessionInfo below).
>
> Is the problem with my .tif files, or is there a problem of
> incompatibility
> with the new version of R and the dependencies, or something else?
>
> Thanks for any light you can shed.
>
> Krys
>
> Here is my code and output:
>
> > BLData <- readIllumina(textType=".txt")
> Found 2 arrays
> Reading pixels of 1863191039_A_1_Grn.tif
> Calculating background
> Sharpening Image
> Calculating foregound
> Background correcting: method = none
> Reading pixels of 1863191039_A_2_Grn.tif
> Calculating background
> Sharpening Image
> Calculating foregound
> Background correcting: method = none
> > an <- arrayNames(BLData)
> > summary(BLData@beadData[[an[1]]]$G)
>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
> -9547.0     0.0     0.0   371.1   267.5 30110.0
> > summary(BLData@beadData[[an[1]]]$Gb)
>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
>       0       0       0       0       0       0
> >
> > lengthG <- length(BLData@beadData[[an[1]]]$G)
> > lengthG
> [1] 904963
> > myNegatives <-
> length(BLData@beadData[[an[1]]]$G[BLData@beadData[[an[1]]]$G<0])
> > myNegatives
> [1] 169302
> > myZeros <-
> length(BLData@beadData[[an[1]]]$G[BLData@beadData[[an[1]]]$G==0])
> > myZeros
> [1] 360331
> > myPositives <-
> length(BLData@beadData[[an[1]]]$G[BLData@beadData[[an[1]]]$G>0])
> > myPositives
> [1] 375330
> >
>
> Here is my sessionInfo:
>
> R version 2.5.1 (2007-06-27)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] "grid"      "tools"     "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "methods"   "base"
>
> other attached packages:
>    beadarray beadarraySNP  quantsmooth      lodplot     quantreg
> SparseM
>      "1.4.0"      "1.2.0"      "1.2.0"        "1.1"       "4.08"
> "0.73"
>         affy       affyio  geneplotter      lattice     annotate
> Biobase
>     "1.14.2"      "1.4.1"     "1.14.0"    "0.15-11"     "1.14.1"
> "1.14.1"
>        limma
>     "2.10.5"
>
>
> Dr Krystyna A Kelly (Krys)
>
> Department of Pathology
> University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
> Tel: 01223 333331
>
> and
>
> MRC Biostatistics Unit
> Institute of Public Health, Robinson Way, Cambridge CB2 0SR
> Tel: 01223 767408
>
> Email: kak28@cam.ac.uk
>
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