Hi.
On Tue, Oct 28, 2008 at 2:25 PM, Venkat <[EMAIL PROTECTED]> wrote:
>
> Hi:
>
> Is it possible to provide a specific list of probe names (from the SNP
> chip) for the subsetToAvg argument in the QuantileNormalization
> function in order to normalize based only a pre-defined subset?
Yes, because the 'subsetToAvg' argument takes a vector of cell indices
(alt. a scalar in (0,1] to indicate a deterministic fraction of all
cell indices). So, you need to find the cell indices for the units
(==SNPs/CN loci) of interest. If you know the unit indices you can
use getCellIndices(cdf, ...) to get the cell indices. To find the
unit indices based on unit names, you can use indexOf(cdf, ...).
Example:
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> unitNames <- c("SNP_A-4214079", "SNP_A-2001454", "CN_453850")
> units <- indexOf(cdf, names=unitNames);
> str(units);
int [1:3] 1001 1002 980123
> cells <- getCellIndices(cdf, units=units, unlist=TRUE, useNames=FALSE);
> cells <- sort(cells);
> str(cells);
int [1:13] 133501 133502 588881 588882 640619 640620 3418844 4756905 4756
05565 ...
>
> Also there is a QuantileNormalization step in the vignette for the
> total copy number analysis for the 500k chips but not GWS6 chips. Is
> the QuantileNormalization step available and correct for GWS6 chips?
The QuantileNormalization class/method works for any Affymetrix chip type.
There are many different ways to pre-process data out there and the
two vignettes show to different ways.
I should really put up a CRMA (v1) vignette illustrating the exact
steps in the Bengtsson et al. (2008) paper or CRMA preprocessing (our
preferred method) of 500K (and before), but short of time... Although
developed for 500K (before GWS5/6 came out), the CRMA model (with some
modifications) actually applies to GWS5/GWS6 arrays too. If replacing
AvgCnPlm with RlmCnPlm in the GWS6 vignette, you actually have CRMA.
Of course, there are some hidden details taking care of the
multi-enzyme hybridization etc, but the main idea is the same. There
will soon also be a CRMA v2 method that we developed for GWS5/6 (but
will be backward compatible with all generations of SNP/CN chip
types). The major news will be that it also does sequence-based
normalization and is a single-array preprocessing method. Stay
tuned... (there will for sure be a CRMA v2 vignette).
Cheers
Henrik
>
> Thanks,
> Venkat
>
> >
>
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