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
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