Re: Normalizing only a subset of the units (Was: Re: [aroma.affymetrix] Re: Question for custom CDF of ST-Array)
Henrik Bengtsson
first of all, instead of posting lots of different questions in one
message (with a as specific subject line as possible), it is much
better to post one well constrained question per message. It will be
less overwhelming for someone to reply to your message and you will
probably see much faster responses.
On Thu, Jan 28, 2010 at 4:58 PM, branko <b.mi...@lumc.nl> wrote:
> Hi all,
[snip]
> 2) One more related to 1st Q : How to run normalization only on
> ProbeSet classified as “main” ? ( Affymetrix csv file says this
> class has 28829
> Psets in main class) Idea is of course to minimize
> normalization bias of non-main class Psets.
Not sure which normalization method you are referring to, but if it is
quantile normalization, you can specifying which *cells* ("probes")
you want to update/normalize by specifying their *cell index* in
argument 'subsetToUpdate'.
Example:
cdf <- getCdf(csR);
# Say you are interested in the following units.
units <- 1:10000;
# Alt: If you know the names of the units of interest, you can do:
unitNames <- ...
units <- indexOf(cdf, unitNames);
# Get the indices of all cells that are part of these units
cells <- getCellIndices(cdf, units=units, unlist=TRUE);
# Do quantile normalization using only these cells
qn <- QuantileNormalization(csR, subsetToUpdate=cells, tags="*,mainOnly");
[snip]
Hope this helps
Henrik
> Below is my session info .
>
> Hope you can help .
>
> Best regards,
>
> Branko
>
> --------------------------
> Branislav Misovic,
> Department of Toxicogenetics
> Leiden University Medical Center
> PO.box 9600, Building2,Room:T3-11
> 2300 RC Leiden
> The Netherlands
> Phone: +31 71 526 9636
> Mob: 0653135855
> E-mail: b.mi...@lumc.nl
>
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
> Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods
> base
>
> other attached packages:
> [1] abind_1.1-0 aroma.affymetrix_1.3.4
> aroma.apd_0.1.7
> [4] affxparser_1.18.0 R.huge_0.2.0
> aroma.core_1.3.4
> [7] aroma.light_1.15.1 matrixStats_0.1.8
> R.rsp_0.3.6
> [10] R.filesets_0.6.5 digest_0.4.1
> R.cache_0.2.0
> [13] R.utils_1.2.4 R.oo_1.6.6
> EBImage_3.2.0
> [16] R.methodsS3_1.0.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
>
>
>
>
>
> --------------------------
> Branislav Misovic,
> Department of Toxicogenetics
> Leiden University Medical Center
> PO.box 9600, Building2,Room:T3-11
> 2300 RC Leiden
> The Netherlands
> Phone: +31 71 526 9636
> Mob: 0653135855
> E-mail: b.mi...@lumc.nl
>
> --
> 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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