Search
Question: Analysis of Affy-data from amplified RNA
0
gravatar for Rafael A. Irizarry
9.9 years ago by
Rafael A. Irizarry2.3k wrote:
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?). > >
ADD COMMENTlink written 9.9 years ago by Rafael A. Irizarry2.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 222 users visited in the last hour