[BioC] beadarray, bash, hulk, excludeBrihtBeadNeighbors, et al -- how to use practically?

[Anand Patel]

OK.  After having used beadarray to get very good results from
bead-level data, I've recently read all of
the work on the multiple artifact removal methods worked out by the
Cambridge group (refs at end of email).

Indeed, I may have read them a bit too many times.  My question is
based on figure 5 from the spatial
phenomena paper -- the workflow:
http://www.biomedcentral.com/content/supplementary/1471-
2105-11-208-s5.pdf -- link to the paper =
http://www.biomedcentral.com/1471-2105/11/208 .

As of this moment, I have several questions:
1.  In which sequence should one peform the steps in the workflow with
respect to BASH and HULK?
2.  "While BASH removes beads from the analysis, HULK adjusts the
values of the beads left after
BASHing, and combination of the two tools requires care." -- how
should one combine these tools with
the material in the spatial phenomena paper?
3.  Does one run generateNeighbours before running the supplemental scripts
"excludeBrightBeadNeighbours", "nearNonDecodedClusters", and
"deviationFromGrid"?
4.  How does one set weights for all of those abnormal occurrences?
There's no worked example using
everything, just individual demonstrations.

There's an amazing amount of work (as cited above), and I've already
used HULK successfully for several
analyses, but the new functions -- they're a bit rough.  EBImage's
readImage throws up all kinds of flags
about the TIFFs -- tags out of order, imagelength missing, etc.
They're valid images though, Preview
and Photoshop both open them correctly . . .

Help is appreciated.

Thanks,
Anand

Refs:
Smith ML, Lynch AG. BeadDataPackR: A Tool to Facilitate the Sharing of
Raw Data from Illumina BeadArray Studies. Cancer Informatics 2010;
2010:217-27.

Smith ML, Dunning MJ, Tavaré S, Lynch AG. Identification and
correction of previously unreported spatial phenomena using raw
Illumina BeadArray data. BMC Bioinformatics 2010; 11:208.

Lynch AG, Smith ML, Dunning MJ, Cairns JM, Barbosa-Morais NL, and
Tavare S (2009). beadarray, BASH and HULK - tools to increase the
value of Illumina BeadArray experiments. In A. Gusnanto, K.V. Mardia,
& C.J. Fallaize (eds), Statistical Tools for Challenges in
Bioinformatics, pp.33-37. Leeds, Leeds University Press.

Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. BASH: A tool
for managing BeadArray spatial artefacts Bioinformatics Oct 25 Epub
ahead of print [pubmed]

Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S, Ritchie ME.
Statistical issues in the analysis of Illumina data. BMC
Bioinformatics 2008 9:85

Dunning MJ, Thorne NP, Tavaré S. Quality control and low-level
statistical analysis of Illumina BeadArrays. REVSTAT - Statistical
Journal, Volume 4, Number 1, March 2006, pages 1-30

Anand C. Patel, MD, MS Bioinformatics
Assistant Professor of Pediatrics and Medicine
Division of Allergy/Pulmonary Medicine
Department of Pediatrics
Washington University School of Medicine
660 South Euclid Ave, Campus Box 8052
St. Louis, MO 63110
acpatel at wustl.edu
acpatel at gmail.com