Hi.
On Tue, Jun 21, 2011 at 9:30 AM, Kai <wangz...@gmail.com> wrote:
> Hi Henrik,
>
> Thanks for your help. However, I got some errors when trying our what
> you have suggested. I think the problem was that: when I did
>
> cns <- CbsModel(dsR,dsP);
>
> The sample order in "cns" is no longer the same as that in "dsR" and
> "dsP". So is there a way to change the sample name in dsR, since after
> the CbsModel is constructed, it is difficult to figure out which
> sample is which.
Yes, I think the default
>
> Also, the error message from setAlias() seems to suggest that this
> function can only change the name of individual sample, not a sample
> set. Is this correct?
Yes, that is a correct error message. I'm sorry, I did a mistake;
setAlias() is for renaming the "data set" name not the individual
samples. So, scrap all my suggestions about using setAlias() for what
you are trying to do. Instead...
1. The names used in the ChromosomeExplorer ('ce') are those given by
getNames(ce) which in turn equals getNames(getModel(ce)) where
getModel(ce) is the CbsModel, that is, getNames(cns) is what is used
by ChromosomeExplorer.
2. You can tweak the behavior of getNames(cns) such that in turn calls
getPairedNames(cns). This is still an unofficial tweak, so you have
to do the following to activate it:
cns$.usePairedNames <- TRUE;
Now, when you call getNames(ce), which returns getNames(cns), which in
turn returns getPairedNames(cns).
3. The default behavior of getPairedNames() is to return names of type
(i) "GSM226871vsGSM226870" when there is matched reference sample,
whereas it returns (ii) "GSM226867" when the reference samples is the
average of a pool. In other words, in your case you should get names
of type (ii) whenever you have 'dfRef' as the reference.
Let me know if this works for you
Henrik
PS. If the above is not enough, there is even a way to customize how
the paired names are generated. See the source code
print(getPairedNames.CopyNumberChromosomalModel) on what is going on.
Note however that this is a very unofficial solution which may change
in the future.
>
> Thank you again for your help. Below are the details of my codes and
> the error message I got.
>
> Best,
> Kai
>
>> library("aroma.affymetrix");
>> # Preprocessing using CRMAv2
>> dataSet = "Resistant_model";
>> chipType = "GenomeWideSNP_6";
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
>> dsC = doCRMAv2(dataSet, cdf=cdf);
>> getNames(dsC)
> [1] "Parental" "Resistant"
>
>> # paired analysis
>> idxP <- match("Parental", getNames(dsC));
>> dsP <- extract(dsC, idxP);
>> getNames(dsP)
> [1] "Parental"
>
>> idxR <- match("Resistant", getNames(dsC));
>> dsR <- extract(dsC, idxR);
>> getNames(dsR)
> [1] "Resistant"
>
>> # unpaired analysis
>> ds <-
>> AromaUnitTotalCnBinarySet$byName("SNP6_HAPMAP_FEMALE",tags="ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY",
>> chipType=chipType);
>> # get Hapmap average file
>> dfRef <- getAverageFile(ds, verbose=verbose);
>> # combine paired and unpaired analysis
>> dfRefList <- rep(list(dfRef), times=nbrOfArrays(dsC));
>> dsRef <- AromaUnitTotalCnBinarySet(dfRefList);
>> getNames(dsRef)
> [1] ".average-signals-median-mad" ".average-signals-median-mad"
>
>> append(dsR,dsC);
>> getNames(dsR)
> [1] "Resistant" "Parental" "Resistant"
>
>> append(dsP,dsRef);
>> getNames(dsP)
> [1] "Parental" ".average-signals-median-mad"
> [3] ".average-signals-median-mad"
>
> ### Everything up to this point is fine ###
>
>> cns <- CbsModel(dsR,dsP);
>> getNames(cns)
> [1] "Parental" "Resistant" "Resistant"
>
> ### Now it seems that the "CbsModel" has re-ordered the samples ####
>
>> ce <- ChromosomeExplorer(cns);
>> names <- getNames(ce);
>> names
> [1] "Parental" "Resistant" "Resistant"
>
> ### Again, samples in "ce" are ordered according to "cns", not "dsR"
> and "dsP" ###
>
>> is_hapmap <- (getNames(dsP)==getName(dfRef));
>> names[is_hapmap] <- sprintf("%s-vs-HapMap", names[is_hapmap]);
>> names
> [1] "Parental" "Resistant-vs-HapMap" "Resistant-vs-HapMap"
>
>> setAlias(ce,names);
>> Error in list(`setAlias(ce, names)` = <environment>, `setAlias.Explorer(ce,
>> names)` = <environment>, :
>
> [2011-06-21 09:14:47] Exception: Number of elements in argument
> 'alias' is out of range [0,1]: 3
> at throw(Exception(...))
> at throw.default(sprintf("Number of elements in argument '%s' is out
> of range
> at throw(sprintf("Number of elements in argument '%s' is out of
> range [%d,%d]:
> at getVector.Arguments(static, s, length = length, .name = .name)
> at getVector(static, s, length = length, .name = .name)
> at getCharacters.Arguments(static, ..., length = length)
> at getCharacters(static, ..., length = length)
> at getCharacter.Arguments(static, filename, nchar = nchar, .name
> = .name)
> at getCharacter(static, filename, nchar = nchar, .name = .name)
> at method(static, ...)
> at Arguments$getFilename(alias)
> at setAlias.Explorer(ce, names)
> at setAlias(ce, names)
>
> On Jun 17, 11:48 am, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> Hi.
>>
>>
>>
>> On Fri, Jun 17, 2011 at 10:05 AM, Kai <wangz...@gmail.com> wrote:
>> > Hi Henrik,
>>
>> > Thank you very much for your reply. What you have suggested works,
>> > with the only problem being that there are now repeated sample names
>> > such that the links generated by ChromosomeExplorer don't work
>> > properly. I think this is because that I have analyzed the same sample
>> > twice, once w.r.t the matched parental DNA (paired analysis), the
>> > other time w.r.t. the Hapmap average (unpaired analysis). So my
>> > question is whether there is a way I can change the names of datasets
>> > in a AromaUnitTotalCnBinarySet. My current codes look like the
>> > following:
>>
>> > library("aroma.affymetrix");
>> > # Preprocessing using CRMAv2
>> > dataSet = "Resistant_model";
>> > chipType = "GenomeWideSNP_6";
>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
>> > dsC = doCRMAv2(dataSet, cdf=cdf);
>> > # paired analysis
>> > idxP <- match("Parental", getNames(dsC));
>> > dsP <- extract(dsC, idxP);
>> > idxR <- match("Resistant", getNames(dsC));
>> > dsR <- extract(dsC, idxR);
>>
>> Here I would add a "sanity check" just in case:
>>
>> stopifnot(nbrOfArrays(dsP) == nbrOfArrays(dsR));
>>
>> because that is what you assume when you setup CbsModel() below, correct?
>>
>> > # unpaired analysis
>> > ds <- AromaUnitTotalCnBinarySet$byName("SNP6_HAPMAP_FEMALE",
>> > tags="ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY", chipType=chipType);
>> > # get Hapmap average file
>> > dfRef <- getAverageFile(ds, verbose=verbose);
>> > # combine paired and unpaired analysis
>> > dfRefList <- rep(list(dfRef), times=2);
>> > dsRef <- AromaUnitTotalCnBinarySet(dfRefList);
>>
>> Here you create a data set 'dsRef' with *two* copies of the
>> HapMap-pooled reference file...
>>
>> > append(dsR,dsC);
>> > append(dsP,dsRef);
>>
>> ...and from those two lines, I suspect it is because 'dsC' contains
>> *two* files, correct? If so, I would replace the above to be:
>>
>> dfRefList <- rep(list(dfRef), times=nbrOfArrays(dsC));
>>
>> If this is not what you've intended, I think there is something wrong.
>>
>> > cns <- CbsModel(dsR,dsP);
>> > ce <- ChromosomeExplorer(cns);
>> > process(ce, verbose=verbose);
>>
>> > The problem arose when I appended "dsC" to "dsR": since "dsC" already
>> > contains "dsR", the resulting variable will contain three datasets:
>> > (dsR, dsR, dsP).
>>
>> Yes.
>>
>> > The corresponding reference set contains (dsP,
>> > Hapmap, Hapmap).
>>
>> So, comment above.
>>
>> > These three comparisons are what I intended to do,
>> > but the two "dsR"s will have the same name which has caused the
>> > ChromosomeExplorer display problem.
>>
>> Correct.
>>
>> The easiest is to use the setAlias() method on the ChromosomeExplorer
>> object, e.g.
>>
>> names <- getNames(ce);
>> isHapMap <- (getNames(dsP) == getName(dfRef));
>> names[isHapMap] <- sprintf("%s-vs-HapMap", names[isHapMap]);
>> setAlias(ce, names);
>>
>> Hope this helps
>>
>> Henrik
>>
>> > Any help you can provided here is
>> > much appreciated!
>>
>> > Best,
>> > Kai
>>
>> > On May 25, 6:20 pm, Henrik Bengtsson <henrik.bengts...@aroma-
>> > project.org> wrote:
>> >> Hi,
>>
>> >> sorry for the delay - your question required some extra explanation.
>>
>> >> On Mon, May 23, 2011 at 2:37 PM, Kai <wangz...@gmail.com> wrote:
>> >> > Hi, Henrik,
>>
>> >> > I have some Affymetrix SNP6 data on a resistant cell line model after
>> >> > compound treatment. I want to do a paired analysis comparing the
>> >> > resistant cell line data to the parental. To make sure that the
>> >> > changes I see in the paired analysis is indeed acquired aberrations,
>> >> > not simply a magnitude change between the resistant and parental, I
>> >> > also want to analyze the resistant and parental data separately
>> >> > against a common reference (e.g. Hapmap). So my question is how I can
>> >> > combine both a paired and an unpaired analysis in aroma affymetrix/cn.
>>
>> >> > Some codes I have for the paired analysis are as follows:
>>
>> >> > library("aroma.affymetrix");
>> >> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
>>
>> >> > options(digits=4);
>> >> > dataSet = "Resistant_model";
>> >> > chipType = "GenomeWideSNP_6";
>> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
>>
>> >> > dsC = doCRMAv2(dataSet, cdf=cdf, verbose=verbose);
>> >> > print(dsC);
>>
>> >> > # paired analysis
>> >> > idxP <- match("Parental", getNames(dsC));
>> >> > dsP <- extract(dsC, idxP);
>>
>> >> > idxR <- match("Resistant", getNames(dsC));
>> >> > dsR <- extract(dsC, idxR);
>>
>> >> > cns2 <- CbsModel(dsR,dsP);
>> >> > print(cns2);
>>
>> >> So, first thing to note is that you are here by specifying (dsR, dsP)
>> >> "manually" telling CbsModel how to pair the samples, i.e. first sample
>> >> in dsR will be coupled with the first sample in dsP, the second with
>> >> each other and so on.
>>
>> >> > ce2 <- ChromosomeExplorer(cns2);
>>
>> >> Here, ChromosomeExplorer is just doing whatever CbsModel is setup to
>> >> do, so it has nothing to do with ChromosomeExplorer, i.e. the study
>> >> design is specified when you setup the CbsModel.
>>
>> >> > print(ce2);
>>
>> >> > process(ce2, verbose=verbose);
>>
>> >> > I have also loaded a set of preprocessed Hapmap samples as follows:
>>
>> >> > ds <- AromaUnitTotalCnBinarySet$byName("SNP6_HAPMAP_FEMALE",
>> >> > tags="ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY",
>> >> > chipType="GenomeWideSNP_6");
>> >> > print(ds);
>>
>> >> > dsRef <- getAverageFile(ds, verbose=verbose);
>> >> > print(dsRef);
>>
>> >> You should really name this 'dfRef" to indicate that it is a data
>> >> *file* (and not a data set).
>>
>> >> Ok, so here you have (i) a data set 'ds' and (ii) a data *file*
>> >> 'dfRef'. What is useful to understand is that when you do:
>>
>> >> seg <- CbsModel(ds);
>>
>> >> you are implicitly doing:
>>
>> >> seg <- CbsModel(ds, dfRef);
>>
>> >> which in turn corresponds to specifying:
>>
>> >> # Create a data set of replicated reference samples
>> >> dfRefList <- rep(list(dfRef), times=length(ds));
>> >> dsRef <- AromaUnitTotalCnBinarySet(dfRefList);
>>
>> >> # Request a "paired" segmentation
>> >> seg <- CbsModel(ds, dsRef);
>>
>> >> Note, you now have two CbsModel:s where both do "paired" segmentation.
>> >> What is left to do is make these two into one CbsModel:
>>
>> >> # Append the latter data sets to the first ones
>> >> append(dsR, ds);
>> >> append(dsP, dsRef);
>>
>> >> # Vola
>> >> seg <- CbsModel(dsR, dsP);
>>
>> >> Hope this helps
>>
>> >> /Henrik
>>
>> >> > I was wondering whether there is a way that will allow me to construct
>> >> > a AromaUnitTotalCnBinarySet consisting of: 1) Resistant, 2) Resistant
>> >> > and 3) Parental; then compare it to another reference set consisting
>> >> > of: 1) Parental, 2) Hapmap and 3) Hapmap.
>>
>> >> > I understand that I can do the paired and unpaired analysis
>> >> > separately, but I want to generate one ChromsomeExplorer report
>> >> > consisting both of them so I can easily compare across them visually.
>> >> > Any help you can provide is much appreciated.
>>
>> >> > Best,
>> >> > Kai
>>
>> >> > --
>> >> > 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
>> >> > websitehttp://www.aroma-project.org/.
>> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> >> > To unsubscribe and other options, go
>> >> > tohttp://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 websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://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/
>
--
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/
