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.
>>
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>> > 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
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