Hi,
if you do:
library("aroma.affymetrix");
setOption(aromaSettings,"memory/ram", 50.0);
ram <- getOption(aromaSettings,"memory/ram");
print(ram);
do you get NULL or 50.0? My guess is NULL, which would explain it.
If so, try to update the aroma framework (minor fixed have been done
recently) by:
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
BTW, you're running a rather old version of R - I recommend that you
update it. Lots of (good) things
[http://cran.r-project.org/src/base/NEWS] have changed since.
/Henrik
On Mon, Aug 29, 2011 at 6:01 AM, feugeas jean-paul
<jean-paul.feug...@sls.aphp.fr> wrote:
> Hello,
> thank you very much for your answer. I have now found a way to increase the
> RAM scale factor.
> It actually works when I write the RAM scale factor inside the function like
> this :
> fit(plm,ram=50,verbose=verbose)
> But it does not work If I write the RAM scale factor like this :
> setOption(aromaSettings,"memory/ram",50.0)
> fit(plm,verbose=verbose)
> In that case it always takes 1 as RAM scale factor.
> Sincerly yours
> Jean-Paul
>
>
> For information, here is my sessioninfo()
> R version 2.11.0 (2010-04-22)
> x86_64-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=en_US.utf8
> [9] LC_ADDRESS=en_US.utf8 LC_TELEPHONE=en_US.utf8
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=en_US.utf8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.1.0 aroma.apd_0.1.8 affxparser_1.20.0
> [4] R.huge_0.2.2 aroma.core_2.1.0 aroma.light_1.20.0
> [7] matrixStats_0.2.2 R.rsp_0.5.4 R.cache_0.4.2
> [10] R.filesets_1.0.2 digest_0.5.0 oligo_1.12.2
> [13] oligoClasses_1.10.0 Biobase_2.8.0 R.utils_1.7.5
> [16] R.oo_1.8.0 R.methodsS3_1.2.1 rkward_0.5.3
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2
> [4] Biostrings_2.16.9 DBI_0.2-5 genefilter_1.30.0
> [7] IRanges_1.6.17 preprocessCore_1.10.0 RSQLite_0.9-4
> [10] splines_2.11.0 survival_2.35-8 tools_2.11.0
> [13] xtable_1.5-6
>
>>
>
>
> ----- Message d'origine -----
> De: Henrik Bengtsson <henrik.bengts...@aroma-project.org>
> Date: Dimanche, Août 28, 2011 2:02 am
> Objet: Re: [aroma.affymetrix] RAM scale factor
> À: aroma-affymetrix@googlegroups.com
>
>
>> Hi,
>>
>> sorry for the delay. This should work, but before diving into serious
>> troubleshooting, could you please report your sessionInfo() so we know
>> which versions of packages etc you are using?
>>
>> /Henrik
>>
>> On Wed, Aug 17, 2011 at 4:38 AM, feugeas jean-paul
>> <jean-paul.feug...@sls.aphp.fr> wrote:
>> > Hello,
>> > I am currently trying to analyze data from 3223 arrays (expression
>> arrays, U133 plus 2) with the following code :
>> >
>> > verbose<-Arguments$getVerbose(-8,timestamp=TRUE)
>> > setOption(aromaSettings,"memory/ram",300.0)
>> > cdf<-AffymetrixCdfFile$fromFile("/media/lapino/Rabitt/compilation/ThBigCompil/2_arrays/annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf")
>> > cs <- AffymetrixCelSet$byName("jp", cdf=cdf)
>> > bc <- GcRmaBackgroundCorrection(cs,type="affinities");
>> > csB <- process(bc,verbose=verbose);
>> > qn <- QuantileNormalization(csB, typesToUpdate="pm");
>> > csN <- process(qn);
>> > plm <- RmaPlm(csN, flavor="oligo");
>> > fit(plm,verbose=verbose)
>> >
>> > at that point, the number of chunks is always 866 as it was with a
>> RAM scale factor = 1 although RAM scale factor = 300 as it is
>> indicated here :
>> >
>> > RmaPlm:
>> > Data set: jp
>> > Chip type: HG-U133_Plus_2
>> > Input tags: GRBC,QN
>> > Output tags: GRBC,QN,RMA,oligo
>> > Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr
>> "oligo"; treatNAsAs: chr "weights").
>> > Path: plmData/jp,GRBC,QN,RMA,oligo/HG-U133_Plus_2
>> > RAM: 0.01MB
>> > 20110817 13:01:43| Started: 20110817 12:17:56
>> > 20110817 13:01:43| Estimated time left: 37862.0min
>> > 20110817 13:01:43| ETA: 20110912 20:03:41
>> > 20110817 13:01:43| Fitting chunk #1 of 866...done
>> > 20110817 13:01:43| Fitting chunk #2 of 866...
>> > 20110817 13:01:43| Units:
>> > int [1:62] 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 ...
>> > 20110817 13:01:43| Reading probe intensities from 3223 arrays...
>> > 20110817 13:01:43| Identifying CDF cell indices...
>> >
>> >
>> > Is there a mean to reduce the number of chunks ?
>> >
>> > Thank you in advance for your help
>> >
>> > Sincerly yours
>> >
>> > Jean-Paul
>> >
>> > --
>> > 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
>> > To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>> >
>>
>> --
>> 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
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> 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
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
