Hi, slow response but answers below. On Wed, Apr 2, 2014 at 8:20 AM, hr <hr...@nyu.edu> wrote: > Dear Henrik, > > Is there a way to read in CEL.gz files rather than .CEL files?
Unfortunately not, only non-compressed CEL files are supported. This is mainly because the Affymetrix Fusion SDK that we utilize via the 'affxparser' package does not support compressed files. > > Also, do you provide an example (couldn't find one on the aroma homepage) on > how to go from a CDF file and a bunch of CEL files to a final expression > matrix normalized with RMA? Essentially I am looking for the equivalent of: > > > library(affy) > library(annotate) > library(hgu133plus2.db) > > files = c("A.CEL.gz", "B.CEL.gz", "C.CEL.gz") > setwd("datadir") > > eset <- justRMA(filenames = files) > mat <- exprs(eset) > > > What is the most efficient way to do this with Aroma? I've added justRMA() to aroma.affymetrix 2.12.2 so you can do: cs <- AffymetrixCelSet$byName("AbcDataSet", chipType="HG-U133_Plus_2") eset <- justRMA(cs) mat <- exprs(eset) which replicates affy::justRMA() very well. This is done keeping the memory usage constant regardless of the number of arrays during the preprocessing. At the end, before justRMA() returns a Biobase::ExpressionSet it needs to load the *summarized* data in, so then memory becomes an issue, but that hits you order of magnitudes later compared to the probe-level data. For example, on HG-U133_Plus_2 there is 54,675 units and 'eset' contains both signals and standard errors (8+8 bytes), so one array requires ~0.84 MB of RAM. Thus, 1,000 arrays occupies roughly 0.84 GB of RAM. To efficiently being able to manipulate in Bioconductor, you should double or triple the memory requirements. You can install/update to the most recent version of aroma.affymetrix as: source('http://aroma-project.org/R/install#aroma.affymetrix') Hope this helps Henrik > > Many thanks and best wishes! > > Helge > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.