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

[Anand Patel]

>From: Mark Dunning <mark.dunning at ...>
>Subject: Re: beadarray, bash, hulk, excludeBrihtBeadNeighbors, et al -- how to use practically?
>Newsgroups: gmane.science.biology.informatics.conductor
>Date: 2010-11-11 10:39:14 GMT (1 week, 4 days, 11 hours and 26 minutes ago)
>Hi Anand,
>
>Many thanks for your interest in our work on spatial artefacts. Our
>current belief is to do things in the following order
>
>1) Detect the phenomena described in the Smith et al (2010) paper. You
>do need to run generateNeighbours before many of these functions. The
>number of beads detected at this stage should be relatively small, and
>would probably be removed by BASH anyway. However, their presence in
>the BASH calculation might hide other defects that should be removed.
>
>2) BASH to mask artefacts
>
>3) HULK to smooth gradients
>
>The order in which one does BASH and HULK could be a topic for
>research. In cases of severe gradients across the array, you might get
>a lot of beads masked at one edge of the array. However, if HULK were
>run first these beads might be saved.
>
>I guess you've already found the setWeights function in beadarray that
>can save the weights found by BASH to the bead-level object? These
>weights are multiplied by bead intensities when the bead summary data
>are created. Currently we tend to use 0 or 1 as weights but there is
>no reason why you couldn't use other values. A feature of the new
>version of beadarray (version 2.0 and newer) is that you can save
>weights under different names in the bead-level object. It should be
>possible to do a series of tests for aberrant beads, save the results
>separately and then combine in some way to produce the weights used in
>summarisation.

That's the big question -- how to combine all 3 methods in the above sequence?

setWeights (in beadarray 2.0.2) reports having an option to combine
the weights with existing weights, so that seems like it's a step in
this direction.  Actually, if they're 0 or 1 weights, wouldn't simply
combining them include all of the information from both BASH and HULK?

>Could you give more information about the errors you have with
>EBImage? Which version of EBImage are you running? We tried the latest
>of EBImage with the example data for the Smith et al paper and it
>worked fine.

EBImage spouts a lot of warnings and errors, but still completes work.

Thanks,
Anand

>Regards,
>
>Mark
>
>On Sat, Oct 30, 2010 at 12:15 AM, Anand Patel <acpatel at ...> wrote:
>> 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 ...
>> acpatel at ...
>>
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