[BioC] Error mas5calls(AffyBatchData) for Hu6800 arrays, - help,

Benjamin Otto b.otto at uke.uni-hamburg.de
Wed Jan 18 16:03:08 CET 2006

Hi Saurin,

the Hu6800 cdf environment doesn't have a stored alpha1 and alpha2 value.
Try the command

$> MASoutput <-  mas5calls(AffyBatchData,alpha1=0.05,alpha2=0.065)

if you would like to use an alpha1 value of 0.05 and alpha2 of 0.065 for
example. This should work, have a look at the help page of mas5calls.
Unfortunately this solution doesn't work with the
"pairwise.comparison"-method because that one doesn't accept a manual
definition of the alpha values. Maybe somebody else has got an idea how to
work around the problem with that function?

Just as a remark:

$> getAlpha1("hgu133plus2cdf")

returns the current alpha1 value stored in the hgu133plus2cdf and is equal

$> get("alpha", envir = .qcEnv)["hgu133plus2cdf", "alpha1"]

The following command displays both alpha values for all registred cdf
environments providing them:

$> get("alpha", envir = .qcEnv)

Maybe there is some way to extend this table manually by desired entries or
even update the goal cdf environment file permanent. But currently I can't
tell how...


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Saurin D.
> Jani
> Sent: 17 January 2006 16:15
> To: bioconductor
> Subject: [BioC] Error mas5calls(AffyBatchData) for Hu6800 arrays, -
> help,
> Dear BioC,
> Has any one got error in mas5calls(AffyBatchData) for Hu6800 arrays?
> I get below error:
> MASoutput <-  mas5calls(AffyBatchData)
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in if (y < alpha1) { : missing value where TRUE/FALSE needed
> How can I resolve this error?
> Thank you in advance,
> Saurin
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> Bioconductor at stat.math.ethz.ch
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