I am trying to use beadarray to import Illumina iScan data but I seem to be missing some detail earlier in the process than others who have posted to this mailing list. I sent the University of Cambridge instructions http://www.compbio.group.cam.ac.uk/Resources/illumina/index.html to the group that created the data and I got the .tif, _perBeadFile.txt , Swath1_Grn.locs , Swath2_Grn.locs , and the Metrics.txt file back from them.

I ran  processSwathData(inputDir='7911747003',twoColour=F,fullOutput=T,textstring="_perBeadFile.txt") which gave me the swath1.txt and swath2.txt files I expected. They look like this
Code    Grn    GrnX    GrnY    Weight
10008    528    261.5272    28315.51    1
10008    541    855.4937    29410.51    1
10008    388    912.4988    18482.5    1
10008    500    1188.497    17681.5    1
10008    545    236.5013    14603.5    1
10008    424    341.505    4820.499    1
10008    573    400.0708    4815.309    1
10008    440    921.5268    2849.498    1
10008    617    1717.477    23031.51    0.5
10008    604    1660.978    14248.01    0.5
10008    583    2007.477    14506.5    0.5
10008    738    1939.5    7212.493    0.5
10010    100    1198.26    29319.64    1
10010    84    1197.688    29261.74    1

Then I ran:
> Illumina.data <- readIllumina()
(all defaults with working directory folder containing processSwathData output files 7911747003_A-Swath1.txt, 7911747003_A-Swath2.txt, 7911747003_B-Swath1.txt ...)

and I got the error message:

The specified sampleSheet  c:\Users\craig\Desktop\Current Projects\Lama\Test\sampleSheet.csv  was not found
No sample sheet was specified. Trying to read all Illumina files inc:\Users\craig\Desktop\Current Projects\Lama\Test
Error in analyseDirectory(dir = rootdir, sectionNames = sectionNames,  :
  iScan data detected
This must first be processed with the function processSwathData()
In addition: Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="sampleSheet.csv": The system cannot find the file specified


Can anyone tell me what I am doing wrong and why readIllumina is still upset with me having iScan data? Secondly, will I have to make a sampleSheet.csv/targets file and what is the expected format for that?

if necessary I can probably put together some of the data to reproduce the problem but I suspect I am just being dumb and missed some detail(it's my first time seeing Illumina data). Any help would be appreciated.

Craig

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] beadarray_2.6.0    ggplot2_0.9.1      Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.18.1 BeadDataPackR_1.8.0  colorspace_1.1-1
 [4] DBI_0.2-5            dichromat_1.2-4      digest_0.5.2
 [7] grid_2.15.0          IRanges_1.14.3       labeling_0.1
[10] limma_3.12.0         MASS_7.3-18          memoise_0.1
[13] munsell_0.3          plyr_1.7.1           proto_0.3-9.2
[16] RColorBrewer_1.0-5   reshape2_1.2.1       RSQLite_0.11.1
[19] scales_0.2.1         stats4_2.15.0        stringr_0.6
[22] tools_2.15.0




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