Hello, 
I am currently trying to analyze data from affymetrix human promoter tiling array with the following code :
> library(aroma.affymetrix)


> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> chipType <- "Hs_PromPR_v02"
> cdf <- AffymetrixCdfFile$byChipType(chipType)
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/Hs_PromPR_v02
Filename: Hs_PromPR_v02.cdf
Filesize: 61.95MB
Chip type: Hs_PromPR_v02
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2166x2166
Number of cells: 4691556
Number of units: 23155
Cells per unit: 202.62
Number of QC units: 0
> s <- AffymetrixCelSet$byName("DS", cdf=cdf)
> mn <- MatNormalization(s)


> csN <- process(mn, verbose=verbose)
20121126 20:48:51|Normalization data set for probe-sequence effects...
20121126 20:48:51| Locating probe-sequence annotation data...
20121126 20:48:51|  Getting AromaCellSequenceFile...
20121126 20:48:51|   Locating...
20121126 20:48:51|    Chip type: Hs_PromPR_v02
20121126 20:48:51|    Number of cells: 4691556
20121126 20:48:51|    Locating AromaCellSequenceFile...
20121126 20:48:51|     Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
20121126 20:48:51|    Locating AromaCellSequenceFile...done
20121126 20:48:51|   Locating...done
   AromaCellSequenceFile:
   Name: Hs_PromPR_v02
   Tags: 
   Full name: Hs_PromPR_v02
   Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
   File size: 116.33 MB (121980713 bytes)
   RAM: 0.00 MB
   Number of data rows: 4691556
   File format: v1
   Dimensions: 4691556x26
   Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
   Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
   Footer: <createdOn>20081204 16:42:56 EST</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
   Chip type: Hs_PromPR_v02
   Platform: Affymetrix
20121126 20:48:51|  Getting AromaCellSequenceFile...done
20121126 20:48:51| Locating probe-sequence annotation data...done
20121126 20:48:51| Locating match scores annotation data...
20121126 20:48:51|  Locating AromaCellMatchScoreFile...
20121126 20:48:51|   Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm
   AromaCellMatchScoreFile:
   Name: Hs_PromPR_v02
   Tags: 
   Full name: Hs_PromPR_v02
   Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm
   File size: 4.47 MB (4691738 bytes)
   RAM: 0.00 MB
   Number of data rows: 4691556
   File format: v1
   Dimensions: 4691556x1
   Column classes: integer
   Number of bytes per column: 1
   Footer: <createdOn>20081204 16:55:16 EST</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
   Chip type: Hs_PromPR_v02
   Platform: Affymetrix
20121126 20:48:52|  Locating AromaCellMatchScoreFile...done
20121126 20:48:52| Locating match scores annotation data...done
20121126 20:48:52| Reading 'non-missing' cells to fit...
20121126 20:48:54|  Cells to fit:
   int [1:4200512] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ...
20121126 20:48:54| Reading 'non-missing' cells to fit...done
20121126 20:48:54| Normalizing 1 arrays...
20121126 20:48:54|  Path: probeData/DS,MN,lm/Hs_PromPR_v02...
20121126 20:48:55|   Number cells per chunk: 1000001
20121126 20:48:55|   Fitting chunk #1 of 5...
20121126 20:48:55|    Cells: 
     int [1:1000001] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ...
20121126 20:48:55|    Reading design matrix...
20121126 20:48:55|     Retrieving design matrix...
20121126 20:48:55|      Cells:
       int [1:1000001] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ...
20121126 20:48:55|      Locating probe-sequence annotation data...
20121126 20:48:55|       Getting AromaCellSequenceFile...
        AromaCellSequenceFile:
        Name: Hs_PromPR_v02
        Tags: 
        Full name: Hs_PromPR_v02
        Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
        File size: 116.33 MB (121980713 bytes)
        RAM: 0.00 MB
        Number of data rows: 4691556
        File format: v1
        Dimensions: 4691556x26
        Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
        Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
        Footer: <createdOn>20081204 16:42:56 EST</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
        Chip type: Hs_PromPR_v02
        Platform: Affymetrix
20121126 20:48:55|       Getting AromaCellSequenceFile...done
20121126 20:48:55|      Locating probe-sequence annotation data...done
20121126 20:48:55|      Locating match scores annotation data...
20121126 20:48:55|      Locating match scores annotation data...done
20121126 20:48:55|      Reading sequence matrix...
20121126 20:48:55|       Reading sequence matrix...
20121126 20:48:55|        Reading data frame...
20121126 20:48:55|         Allocating data object...
20121126 20:48:55|          Number of rows: 1000001
20121126 20:48:55|          Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
          'data.frame': 1000001 obs. of  25 variables:
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
           $ : raw  00 00 00 00 ...
20121126 20:48:55|         Allocating data object...done
20121126 20:48:55|         Reading data...
20121126 20:48:59|         Reading data...done
20121126 20:48:59|        Reading data frame...done
20121126 20:48:59|        Coerce to a character matrix...
20121126 20:49:00|        Coerce to a character matrix...done
20121126 20:49:00|       Reading sequence matrix...done
20121126 20:49:00|      Reading sequence matrix...done
20121126 20:49:00|      Reading match scores...
20121126 20:49:01|       Allocating data object...
20121126 20:49:01|        Number of rows: 1000001
20121126 20:49:01|        Column classes: integer
        'data.frame':   1000001 obs. of  1 variable:
         $ : int  0 0 0 0 0 0 0 0 0 0 ...
20121126 20:49:01|       Allocating data object...done
20121126 20:49:01|       Reading data...
20121126 20:49:01|       Reading data...done
20121126 20:49:01|      Reading match scores...done
20121126 20:49:01|      Constructing design matrix...
Error: cannot allocate vector of size 618.0 Mb
In addition: There were 17 warnings (use warnings() to see them)
20121126 20:49:08|      Constructing design matrix...done
20121126 20:49:08|     Retrieving design matrix...done
20121126 20:49:08|    Reading design matrix...done
20121126 20:49:08|   Fitting chunk #1 of 5...done
20121126 20:49:08|  Path: probeData/DS,MN,lm/Hs_PromPR_v02...done
20121126 20:49:08| Normalizing 1 arrays...done
20121126 20:49:08|Normalization data set for probe-sequence effects...done
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)


locale:
[1] LC_COLLATE=Chinese_People's Republic of China.936  LC_CTYPE=Chinese_People's Republic of China.936   
[3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C                                      
[5] LC_TIME=Chinese_People's Republic of China.936    


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:
 [1] aroma.affymetrix_2.6.0 affxparser_1.28.1      aroma.apd_0.2.3        R.huge_0.4.1           aroma.light_1.28.0    
 [6] aroma.core_2.6.0       matrixStats_0.6.2      R.rsp_0.8.2            R.cache_0.6.5          R.devices_2.1.3       
[11] R.filesets_1.6.0       digest_0.5.2           R.utils_1.18.0         R.oo_1.10.2            R.methodsS3_1.4.2     


> memory.limit()
[1] 1535
> memory.limit(T)
[1] 1077
anyone can help me?should i upgrade my pc hardware? Thanks!!
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