Hi Peter.
On Sun, Aug 31, 2008 at 5:02 AM, PA <[EMAIL PROTECTED]> wrote:
>
> Dear all,
> I am quite new to microarray analysis and R in general and to
> aroma.affymetrix in particular.
> I am trying to use aroma.affymetrix for paired (tumor vs. peripheral
> blood) analysis of total copy number with SNP6.0 arrays.
> The Instructions I find here are for unpaired analysis (SNP6.0). For
> paired analysis I only find an example for 250K array sets.
> So far my strategy was to follow the SNP6.0 example until (including)
> PCR fragment length normalization. After that I thought to continue
> with "Identificaiton of copy-number regions in tumor-normal pairs"
> from the 250K example page.
> My problem now: I have not quite understood yet how to adapt the
> commands for use with SNP6.0 arrays. How do I specify which samples
> belong together?
If look carefully in the 'Total Copy Number Analysis (5.0 & 6.0)'
vignette you will actually see a short notice on how to do paired
segmentation;
"In order to do paired analysis using the Circular Binary Segmentation
(CBS) method, do:
cbs <- CbsModel(ces1, ces2);
where 'ces1' is a CEL set of test samples and 'ces2' is a CEL set of
the same number of control samples.". Then you just proceed as
"usual". Technically, each of the 'ces1' and 'ces2' sets is a
CnChipEffectSet object. (Compare this with the case when you only
pass 'ces1', then the reference (ces2) will be the pooled average of
'ces1').
Since you preprocess all tumor and normals together (following the
above vignette), you have a CnChipEffectSet named 'cesN'. If you
know the indices of the tumors in this set, say they are:
arrays1 <- c(1,4,6);
Then you can extract these tumors as:
ces1 <- extract(cesN, arrays1);
The 'ces1' object is also a CnChipEffectSet containing these 3 arrays.
Continuing, say the corresponding normals are:
arrays2 <- c(2,3,5);
Then you can get the CnChipEffectSet of the 3 normals as:
ces2 <- extract(cesN, arrays2);
Note that the pairing is specified by ordering of the vectors
'arrays1' and 'arrays2'. The tumor-normal pairs above are (1,2),
(4,3), and (6,5).
You can validate that you get correct pairing by looking at:
pairs <- matrix(c(getFullNames(ces1), getFullNames(ces2)), ncol=2);
colnames(pairs) <- c("tumor", "normal");
print(pairs);
You'll get something like:
tumor normal
[1,] "NA06985,chipEffects" "NA06991,chipEffects"
[2,] "NA06994,chipEffects" "NA06993,chipEffects"
[3,] "NA07019,chipEffects" "NA07000,chipEffects"
So, how do you know the indices of the arrays in the first place? You
can do it manually, by looking at the full names of the arrays in the
complete set 'cesN', e.g.
print(getNames(cesN));
[1] "NA06985,chipEffects" "NA06991,chipEffects" "NA06993,chipEffects"
[4] "NA06994,chipEffects" "NA07000,chipEffects" "NA07019,chipEffects"
Better is to identify them by their names, e.g.
arrayNames1 <- c("NA06985", "NA06994", "NA07019");
arrayNames2 <- c("NA06991", "NA06993", "NA07000");
arrays1 <- indexOf(cesN, arrayNames1);
arrays2 <- indexOf(cesN, arrayNames2);
print(arrays1);
NA06985 NA06994 NA07019
1 4 6
print(arrays2);
NA06991 NA06993 NA07000
2 3 5
Hope this helps
Henrik
> Any help would be greatly appreciated!
> Peter.
> >
>
--~--~---------~--~----~------------~-------~--~----~
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.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
