Hi. I've changed the subject of this thread, because the term "probe tag" is misleading/ambiguous in the context of aroma.
On Fri, Jan 28, 2011 at 1:22 PM, Taku Tokuyasu <tok...@gmail.com> wrote: > Is there a way to get the list of probe category tags used by > QuantileNormalization, and what they denote? E.g. I have been using > qn <- QuantileNormalization(csBC, typesToUpdate="pm") I think you're misunderstanding how the term "tag" is defined. Data sets and a data files (items in data sets) have names and tags. Models/methods process data sets and they generate new data sets often with new tags appended, cf. http://aroma-project.org/definitions/ The above method will take the data set 'csBC' and do quantile normalization on it based on and updating only the PM probes (argument typesToUpdate="pm"). The generated output data set will have a tag appended to the existing ones. Yes, that tag will be "pm" because you used setting typesToUpdate="pm", but it does not mean that argument 'typesToUpdate' specifies a tag. > I've also seen e.g. "mainOnly" in the docs. The "mainOnly" *tag* is from an example I posted in one of my replied. I think it was something like: qn <- QuantileNormalization(csR, typesToUpdate="pm", tags="*,mainOnly") That is just telling the method that the output data set should have tag "mainOnly" appended to the default ones ("*"). The following would be equivalent and maybe more clear: qn <- QuantileNormalization(csR, typesToUpdate="pm", tags=c("*", "mainOnly")) What is happening here is that the use adds a "custom" tag. What it is does not change the function what so ever. The only tag that is interpreted by aroma is "*", which is expanded to be the default set of tags. > I guess they are coming > from the cdf somehow, or constructed by the user - any hints on how to > get/manipulate these would appreciated. Yes, what is defined as a perfect-match (PM) or a mismatch (MM) probe is given by the CDF file. > Also, getTags() on various > aroma objects did not coming up with anything (yet). As said above, data sets and data files have tags and those tags can be queried using getTags() on such objects. > > I see that in the general case, units to quantile normalize can be > specified by unit name or index, as in > http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/345246c3ba382294?pli=1 Yes, you can either specify which probes (we use the term "cell" in the aroma framework) you want to estimate the QN model on and/or which you want to update. You can specify the *type* of probes, e.g. PM, MM, all. See for instance http://aroma-project.org/node/141. Alternatively, you can specify the indices of the probes, which the thread 'Normalizing only a subset of the units (Was: Re: [aroma.affymetrix] Re: Question for custom CDF of ST-Array)' you are referring to are doing. That thread also shows how to identify those cell indices when you only know the unit names. > > OK, I'll step back to a yet more newbie question: > RmaBackgroundCorrection() adjusts only PM probes by default. What is > the best way to get documentation on the function, so I can see what > PM means here, and what other options are available? help("RmaBackgroundCorrection") - you may also have to follow "..." arguments to see what is passed internally (here to BackgroundCorrection). From the help you also see that internally bg.adjust() of affy package is used for the actually background correction. > Will the code > break if Affy no longer tags their probes as PM? etc. That will never happen. Basically all probes on a chip are perfect-match probes unless they are mismatch probes (and the latter Affymetrix has been discarding in recent generations of chip types). Hope this helps /Henrik > > _Taku > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
