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/