Hi.
On Wed, Feb 23, 2011 at 4:02 PM, Gregory W <greg.d.w...@gmail.com> wrote:
> Hello,
>
> I was hoping to get some information about how to manipulate
> AromaUnitTotalCnBinarySets.
>
> I've already performed CRMAv2 on all the affy platforms in my study.
>
> I load the results into an R session with:
>
>
>> tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" ;
>> dsT <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
>> chipType=chipType) ;
>> print(dsT)
>> dsC <- list() ;
>> dsC$total <- dsT ;
>
>
> I have normal and tumor replicates for a particular patient. I grab
> these data by:
>
>> normals.indx <- match(normal.names,getNames(dsC$total))
>> normals <- extract(dsC$total, normals.indx)
>
> And similarly for the tumors. This is what normals and tumors
> contains:
>
>> normals
> . AromaUnitTotalCnBinarySet:
> . Name: MyStudy
> . Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> . Full name: MyStudy,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> . Number of files: 2
> . Names: Normal_Rep1, Normal_Rep2
> . Path (to the first file): totalAndFracBData/MyStudy,ACC,ra,-
> XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
> . Total file size: 14.35 MB
> . RAM: 0.00MB
>
>
>> tumors
> . AromaUnitTotalCnBinarySet:
> . Name: MyStudy
> . Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> . Full name: MyStudy,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
> . Number of files: 2
> . Names: Tumors_Rep1, Tumors_Rep2
> . Path (to the first file): totalAndFracBData/MyStudy,ACC,ra,-
> XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
> . Total file size: 14.38 MB
> . RAM: 0.00MB
>
>
> I see there's a function getAverageFile that allows me to do this:
>
>> normals.average <- getAverageFile(normals)
>> normals <- newInstance(normals, files=list(normals.average))
>
> and similarly for tumors. Then I can take these results and pass them
> to CbsModel:
>
>> cbs <- CbsModel(tumors, normals)
>
> HOWEVER, even though my replicates are from the same sample, they were
> processed using different protocols. So instead of averaging the
> normals and then averaging the tumors, i would like to take the
> respective ratios and then average the ratios.
>
> I can accomplish this in a round about way by using writeDataFrame and
> loading it back into R and then manipulating the data. But then the
> data isn't in the right format for CbsModel since its been ratio-ized
> and is no longer two AromaUnitTotalCnBinarySets.
>
> 1- Is there a way to perform an average of the ratios and then pass
> this into the CbsModel??
There is not-yet-public approach. The reason why it is "not yet
public" is that the directory and/or file structure may be changed in
the future. However, here is how it goes:
Given your two AromaUnitTotalCnBinarySet:s, you can export total CN
ratios for each tumor-normal pair as:
dsT <- tumors;
dsN <- normals;
dsTCN <- exportTotalCnRatioSet(dsT, dsN, logBase=NULL, verbose=verbose);
which will generate a new AromaUnitTotalCnBinarySet (stored under
"rawCnData/") where the fullnames of the files have format
GSM226867,ref=GSM226872,ratio,total (indicating that the TCN ratios
have been calculated for GSM226867 with GSM226872 as the reference).
Note that this will export TCN on the non-log scale (we avoid
logarithms as far as possible in aroma, especially in the file
formats!).
In order to calculate the average of the T/N samples in this TCN data
set, you can do:
dfAvg <- getAverageFile(dsTCN, verbose=-10);
Importantly, each TCN file i=1,2,...,I contains TCNs calculated as
C_ij = T_ij / N_ij for loci j=1,2,...,J. This means that when you do
the above, the average is calculated as C_j = median_i(C_ij) =
median_i(T_ij / N_ij). If you want to calculate this on the log-ratio
scale(*), you need to do:
dfAvgLog <- getAverageFile(dsTCN, g=log2, h=function(y) 2^y, verbose=-10);
which will calculate the average as C_j = h(median_i(g(C_ij)) =
2^(median_i(log2(C_ij)).
Footnote: (*) Note that since we are using the median to calculate the
average, the two approaches will indeed give identical results, cf.
> diff <- dfAvg[,1] - dfAvgLog[,1]
> summary(diff)
1
Min. :0
1st Qu.:0
Median :0
Mean :0
3rd Qu.:0
Max. :0
In other words, you don't have to bother with g=..., and h=... approach.
Now we're close. The 'dfAvg' object is a file and it has a internal
fullname, e.g. .average-signals-median-mad,72ad79d42f44e60321fc0ad2fbe30a59.
To change this name, do:
# Change the fullname (using a fullname translator)
setFullName(dfAvg, "TumorVsNormal");
Next, before you can pass it to CbsModel, you have wrap the 'dfAvg'
file up in a (single-file) data set, e.g.
dsAvg <- newInstance(dsT, list(dfAvg));
Then do:
# Segmentation model
cbs <- CbsModel(dsAvg, tags="*,TCN,avg");
cbs$.calculateRatios <- FALSE;
and so on.
/Henrik
[snip]
>
> Thank you!
> Greg
>
>
>
> --
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--
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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