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: csSubset1 <- extract(cs, 1:220) rawSubset1 <- extractMatrix(csSubset1, verbose=verbose) csSubset2 <- extract(cs, 221:440) rawSubset2 <- extractMatrix(csSubset2, 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 [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
