Hi.
On Mon, Dec 20, 2010 at 9:10 AM, James F. Reid
<james.r...@ifom-ieo-campus.it> wrote:
> Dear list,
>
> I am currently performing a meta-analysis of different datasets (GEO GSE
> series) and have been writing sample information as dcf format files under
> the 'annotationData/samples' directory however this slows down considerably
> the processing time of running any type of analysis. Here is a short example
> ('testData') involving 10 HG-U133_Plus_2 .CEL files where either no sample
> annotation files are present in the directory or 11 sample annotation files
> are present.
Yes, those sample annotation files do indeed slow things down. The
reason is that for every data set loaded, *all* such files in
annotationData/samples/ are parsed, and each entry of those files are
checked against the data files in the data set you are setting up with
...$byName(). Thus, (i) the more annotation files and (ii) the more
entries they have, the longer it will take.
I am aware of this and that this is suboptimal. It is on my todo list
to come up with a better/faster scheme, and your reports bumps up the
priority a bit, but you shouldn't expect anything to soon. Instead...
If your dataset do not need annotationData/samples/ annotation files,
then exclude that directory. If you are linking to a global
annotationData/ structure for your annotationData/chipTypes/ etc, then
I recommend that you instead create a local annotationData/ directory
and inside that link to annotationData/chipTypes/. This will give you
the option to have a local annotationData/samples/ specific to each
project. That gives you some flexibility.
Hope this helps
Henrik
>
> Is there a way I can reduce this overhead?
>
> Many thanks.
> James
>
> remove ~/.Rcache, start R:
> ## running with 0 sample annotation files
> library("aroma.affymetrix")
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2");
>
> system.time(cs <- AffymetrixCelSet$byName("testData", cdf=cdf));
> user system elapsed
> 0.450 0.020 0.527
>
> exit R, remove ~/.Rcache, start R:
>
> ## running with sample annotations (11 files)
> library("aroma.affymetrix")
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2");
>
> system.time(cs <- AffymetrixCelSet$byName("testData", cdf=cdf));
> user system elapsed
> 16.74 0.10 17.40
>
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets tools methods
> [8] base
>
> other attached packages:
> [1] aroma.affymetrix_1.8.0 aroma.apd_0.1.7 affxparser_1.22.0
> [4] R.huge_0.2.0 aroma.core_1.8.1 aroma.light_1.18.2
> [7] matrixStats_0.2.2 R.rsp_0.4.0 R.cache_0.3.0
> [10] R.filesets_0.9.1 digest_0.4.2 R.utils_1.6.0
> [13] R.oo_1.7.4 R.methodsS3_1.2.1
>
> --
> 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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>
--
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
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