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/
