Hi Carol.
This throws an error because your CDF has a tag ("r3") and there is no way
to send a tag for the CDF file through the AffymetrixCelSet$byName
function. I recommend that you just do this in 2 commands, as you've done
successfully. Alternatively, you can remove the ",r3" from your CDF file
name to remove the tag and that single command should work.
Cheers,
Mark
>
> Hi all,
>
> I'm just starting to analyze expression data form the MoGene-1_0-st-v1
chip using aroma.affymetrix but I'm running into an error for creating a
cs object that I don't really understand.
>
> DATA SET UP:
>
> I started by reading the following to learn about setting up the data
files:
> http://groups.google.com/group/aroma-affymetrix/web/users-guide
>
> Here is my basic set up:
>
> \annotationData\chipTypes\MoGene-1_0-st-v1\MoGene-1_0-st-v1,r3.cdf
\rawData\MGH09\MoGene-1_0-st-v1\<lots o CEL files>
>
>
> WHAT WORKS:
>
>> cdf <- AffymetrixCdfFile$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")
>
> >
>
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