Hi all, I'm just starting to analyze expression data form the MoGene-1_0-st-v1 chip using aroma.affymetrix but I'm running into an error for creating a cs object that I don't really understand.
DATA SET UP: I started by reading the following to learn about setting up the data files: http://groups.google.com/group/aroma-affymetrix/web/users-guide Here is my basic set up: \annotationData\chipTypes\MoGene-1_0-st-v1\MoGene-1_0-st-v1,r3.cdf \rawData\MGH09\MoGene-1_0-st-v1\<lots o CEL files> WHAT WORKS: > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") > print (cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/MoGene-1_0-st-v1 Filename: MoGene-1_0-st-v1,r3.cdf Filesize: 67.42MB Chip type: MoGene-1_0-st-v1,r3 RAM: 0.00MB File format: v3 (text; ASCII) Dimension: 1050x1050 Number of cells: 1102500 Number of units: 35512 Cells per unit: 31.05 Number of QC units: 1 > cs <- AffymetrixCelSet$byName("MGH09", cdf=cdf) > print (cs) AffymetrixCelSet: Name: MGH09 Tags: Path: rawData/MGH09/MoGene-1_0-st-v1 Platform: Affymetrix Chip type: MoGene-1_0-st-v1,r3 Number of arrays: 26 Names: J001_3_11.5, J001_4_11.5, ..., J010_4_16.5 Time period: 2009-09-23 17:51:49 -- 2009-09-23 21:45:31 Total file size: 275.06MB RAM: 0.02MB WHAT DOESN'T WORK: What I tried first, and what I've found in other tutorials, is the folllowing: cs <-AffymetrixCelSet$byName(data name, tags, chipType=chipType) Which I translated to: cs <-AffymetrixCelSet$byName("MGH09", chipType="MoGene-1_0-st-v1") But when I run this I get the error listed below. I'm wondering one approach approach works just fine but this one doesn't. Error in list(`AffymetrixCelSet$byName("MGH09", chipType = "MoGene-1_0- st-v1")` = <environment>, : [2009-10-10 06:55:28] Exception: Could not locate a file for this chip type: MoGene-1_0-st-v1 at throw(Exception(...)) at throw.default("Could not locate a file for this chip type: ", paste(c(chipType, tags), collapse = ",")) at throw("Could not locate a file for this chip type: ", paste(c (chipType, tags), collapse = ",")) at method(static, ...) at AffymetrixCdfFile$byChipType(chipType, nbrOfCells = nbrOfCells) at fromFiles.AffymetrixCelSet(static, path = path, cdf = cdf, ...) at fromFiles(static, path = path, cdf = cdf, ...) at withCallingHandlers(expr, warning = function(w) invokeRestart ("muffleWarning")) at suppressWarnings({ at method(static, ...) at AffymetrixCelSet$byName("MGH09", chipType = "MoGene-1_0-st-v1") --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
