Thanks Mark, It solved the problem.You are a life saver.
Hamid On Fri, Jul 24, 2009 at 7:11 PM, Mark Robinson <mrobin...@wehi.edu.au>wrote: > > Hi Hamid. > > So, the problem you have is that your desired matrix is too large to > fit in memory at once. There are two ways to be able to read in a > subset of data with extractMatrix() that will fit into memory: a > subset of rows (probes, in your case) or a subset of columns (samples). > > To do a subset of rows, you can do something like: > > rowSubset <- 1:10000 > rawSubset <- extractMatrix(cs, cells=rowSubset, verbose=verbose) > > [instead of 1:10000, you may want to use getCellIndices() to pull out > the indices of probes specific to a particular unit (gene?) of interest] > > To do a subset of columns, you can do something like: > > rawSubset1 <- extractMatrix(csSubset1, verbose=verbose) > > Cheers, > Mark > > > > > Hi All, > > > > I have completed back ground correction and normalization of 440 CEL > > files (Each file has 6.4 million rows). When I tried to extract the > > raw data from my CEL files I received the following error. I know > > that this limitation exists in R and C and we cannot have a matrix > > larger that (2^31) which exceeds memory capacity. Now the question > > is can we extract that data of chip 1-220 in one object and 221-440 > > in another object? > > > > The same error is reported when I tried to extract the normalized > > values. I do not want to summarize data as I need to have access to > > data of each probe. > > > > Thanks, > > > > Hamid > > > > > >>> cs > >> AffymetrixCelSet: > >> Name: Mapping_RILs > >> Tags: > >> Path: rawData/Mapping_RILs/Lettuce1b520367 > >> Platform: Affymetrix > >> Chip type: Lettuce1b520367 > >> Number of arrays: 440 > >> Names: 2007_9_28_RIL1_01, 2007_9_28_RIL1_02, ..., > >> SER_TG_new_30ug_02 Time period: 2006-10-17 12:32:30 -- 2009-01-23 > >> 16:52:20 Total file size: 28380.74MB > >> RAM: 0.54MB > >>> raw <- extractMatrix(cs, verbos=verbos) > >> Error in matrix(naValue, nrow = ncells, ncol = nbrOfArrays) : > >> too many elements specified > > > > > > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
