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List:       bioconductor
Subject:    [BioC] maQualityPlots (qpHexbin) question
From:       Rob J Goedman <goedman () mac ! com>
Date:       2005-05-28 15:13:06
Message-ID: 5111D754-6BD6-4FCE-825B-17A5A0FCA108 () mac ! com
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Hi,

Am I using the right versions of arrayQuality and hexbin in BioC 1.6?

Package:       arrayQuality
Version:       1.0.11
Date:          2005-04-10

Package:       hexbin
Version:       1.2.7
Date:          2005-04-06

Working through the 'Quick start guide for marray' I ran into a problem
in step 6 [ library(arrayQuality); maQualityPlots(mraw) ]:

Error in seq.default(0, 1, length = min(17, maxcnt)) :
     length must be non-negative number
In addition: Warning message:
no finite arguments to max; returning -Inf

Traceback shows it is in qpHexbin and looking at the function and
documentation shows bin is an S4 object of class hexbin and mac$cnt
this cannot access the slot 'count'. After fixing that, it runs into:

Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") :
     couldn't find function "hexagons"

Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") :
     couldn't find function "hex.legend"

Which I also changed as in below file qpHexbin.R. The library version  
I've
renamed qpHexbin-orig.R.

Rob




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