[BioC] Analysis of Affy-data from amplified RNA

[Rafael Irizarry]

Samuel,

Thanks for the note. Regarding your request I would recommend you start 
with the bioconductor mailing list for help:

bioconductor Mailing List <bioconductor at stat.math.ethz.ch>

Best wishes,
Rafael

Samuel Wuest wrote:
> Dear Rafa,
> 
> Hope you are fine… I have become a big fan of you when I came across the 
> analysis of Affy-Chips, so thanks for the nice toolboxes you have 
> created so far.
> 
> Although I am not a statistican but a geneticist, I have been chewing 
> for quite a while on the problem of analyzing chips from amplified RNA, 
> and couldn't come up with a solution for making an accurate 
> Present-Absent decision matrix so far…
> 
> I am trying to modify the Affymetrix MAS5 present-absent calls 
> algorithm, adjusting for probe-position bias in the data from amplified 
> samples. I have tried the normal MAS5 and the half-price method, but 
> both of these methods do not cope too well with the amplification bias…
> 
> Up to date, I have the basic ideas and the tools for their 
> implementation/checking the new algorithm, but would need some help on 
> certain issues (details, if interested, see below). I think that your 
> group has the best expertise on the field: do you know anyone that I 
> could contact for a small collaboration?
> 
> Thanks for any help on this, best regards.
> 
> Samuel
> 
> ------------------------------------------------------
> Wuest Samuel
> Smurfit Institute of Genetics
> Trinity College Dublin
> Dublin 2, Ireland
> Phone: +353-1-896 2444
> Mobile: + 353-85-735 5821
> Email: wuests at tcd.ie <mailto:wuests at tcd.ie>
> ------------------------------------------------------
> 
> Details: (supporting illustration are available if necessary: quality 
> control images, 3' positional bias, sensitivity index density, ROC 
> curves of the MAS5 algorithm on my data, etc).
> 
> I am interested in the sexual reproduction of plants, and thus have 
> isolated single cells of reproductive importance in Arabidopsis, such as 
> the egg cell. The samples needed two round of RNA amplification, and 
> there was a slight problem with RNA degradation, so it took me quite a 
> while to get data of suitable quality…
> 
> My goal is the creation of a modified MAS5-calls algorithm that takes 
> into account both probe sensitivity and amplification bias:
> for this, I want to make use of probe-sensitivity indices modelled 
> across multiple chips, all from samples that have been amplified. This 
> allows to estimate both, the probe sensitivity and the amplification 
> bias at the same time.
> 
> The sensitivity-index can be taken as a measure of how reliable a signal 
> from a certain probe actually is.
> So I would change the one-sample Wilcox implemented in the mas5calls 
> into a two sample Wilcox, comparing the measured signals against a 
> null-distribution (consisting of 11 zero-values, one for each probe). 
> For each single probe, an assigned null-value is used for comparison, 
> and this null-value is chosen according to the modelled 
> probe-sensitivity ( e.g. based on quantile information of the respective 
> sensitivity). The new algorithm is assessed using ROC curves that make 
> use of the knowledge that is available so far for the different cell 
> types (true positives) and of a negative probes (where reannotation has 
> led to probes with no targets).
> 
> I would need help on the following points: a) how to create a 
> null-distribution from which to choose null-values and b) general 
> feedback on the method (e.g. is there any major statistical pitfalls in 
> this?).
> 
>