Hi Mario.
I have made some modifications to the reading of probe_tab files and
to the computing of affinities so that this procedure can run now,
either as you have done below by choosing lowly expressed probes, or
(perhaps preferably) by using the 'antigenomic' probes on the array:
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-30); timestampOn(verbose)
cdf<-AffymetrixCdfFile$fromChipType("HuGene-1_0-st-
v1",verbose=verbose,tags="PD")
cs<-AffymetrixCelSet$fromName("tissues",cdf=cdf,verbose=verbose)
bcGc <- GcRmaBackgroundCorrection(cs,
type="affinities",indicesNegativeControl = negativeControlIndices)
csGBC <- process(bcGc,verbose=verbose)
controlIndices <- which(!isPm(cdf))
bc <-
GcRmaBackgroundCorrection
(cs,type="affinities",indicesNegativeControl=controlIndices)
csBC <- process(bc,verbose=verbose,force=TRUE)
I needed to make a CDF file that contained these antigenomic probesets
as they are not present in the binary-converted CDF files I created
previously. I will make available these CDFs once I can test
everything.
Unfortunately, I do not have a good way of testing that my
modifications are doing exactly the right thing, as I am also not
intimately familiar with the gcrma model/code. To be honest, I don't
know of anyone that has successfully run gcrma on these chips or Exon
ST chips, Bioconductor or otherwise. Do you? If so, please let me
know.
These changes can be made available in the next release or possibly
earlier with a patch, but I just want to test the changes first.
Cheers,
Mark
On 27/03/2009, at 10:03 PM, Mario Fasold wrote:
>
> Hi Mark, Hi Richard,
>
> i think gcRMA should work without mismatch probes using the "affinity"
> type correction. There was a similar discussion about exon arrays,
> which are PM-only as well. I have to admit that I have not really
> studied this gcRMA affinity correction procedure, I just like to
> perform correction of sequence-effects to some extend. Here is are the
> steps I performed:
>
> chipType <- "HuGene-1_0-st-v1"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
> cs <- AffymetrixCelSet$byName("foo", cdf=cdf)
>
> celMeans = rowMeans(getIntensities(cs))
> negativeControlIndices = which(celMeans < quantile(celMeans,0.01))
>
> bcGc <- GcRmaBackgroundCorrection(cs, type="affinities",
> indicesNegativeControl = negativeControlIndices)
> csGCBc <- process(bcGc,verbose=verbose)
>
> 20090327 11:42:56|Background correcting data set...
> 20090327 11:42:56| Computing probe affinities...
> 20090327 11:42:56| Computing GCRMA probe affinities for 33252
> units...
> 20090327 11:42:56| Identify PMs and MMs among the CDF cell
> indices...
> logi [1:844550] TRUE TRUE TRUE TRUE TRUE TRUE ...
> Mode TRUE NA's
> logical 844550 0
> 20090327 11:42:57| MMs are defined as non-PMs
> 20090327 11:42:57| Number of PMs: 844550
> 20090327 11:42:57| Number of MMs: 0
> 20090327 11:42:57| Identify PMs and MMs among the CDF cell
> indices...done
> 20090327 11:42:57| Searching for probe sequence file...
> 20090327 11:42:57| Chip type: HuGene-1_0-st-v1
> 20090327 11:42:57| Filename pattern: [._]probe[._]tab$
> [1] "annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-
> v1.probe.tab"
> 20090327 11:42:57| Pathname: annotationData/chipTypes/HuGene-1_0-
> st-
> v1/HuGene-1_0-st-v1.probe.tab
> 20090327 11:42:57| Searching for probe sequence file...done
> 20090327 11:42:57| Pathname of located probe-tab file:
> annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1.probe.tab
> 20090327 11:42:57| Reading tab-delimited sequence file...
> Error in if (any(units < 1)) stop("Argument 'units' contains non-
> positive indices.") :
> missing value where TRUE/FALSE needed
> In addition: Warning message:
> In computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, verbose
> = less(verbose)) :
> NAs introduced by coercion
> 20090327 11:42:57| Computing probe affinities...done
> 20090327 11:42:57|Background correcting data set...done
>
> Thanks, Mario.
>
>
> On Mar 26, 3:55 pm, Richard Beyer <rpbe...@gmail.com> wrote:
>> Hi Mario,
>>
>> I don't think gcrma is going to work with ST arrays since there are
>> no MM
>> probes.
>>
>> Cheers,
>> Dick
>>
>> On 3/24/09, Mario Fasold <fas...@googlemail.com> wrote:
>>
>>
>>
>>> Hi all! I'd like to use gcRMA correction on Human Gene 1.0 ST data.
>>> However, the method GcRmaBackgroundCorrection fails, probably since
>>> the probe_tab file has a slightly different layout for these chips
>>> (see error message below). Is there a way of telling the gcRMA
>>> function to use different columns of the probe_tab file?
>>
>>> Best, Mario.
>>
>>> Reading tab-delimited sequence file...
>>> Error in if (any(units < 1)) stop("Argument 'units' contains non-
>>> positive indices.") :
>>> missing value where TRUE/FALSE needed
> >
------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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