[BioC] RE: maQualityPlots (qpHexbin) question

[Paquet, Agnes]

Hi Rob,

Unfortunately some features of arrayQuality are not compatible with versions of Hexbin greater than 1.0.10 at the moment. The best way to solve this problem would be to install hexbin 1.0.10 either from Bioconductor 1.5 or from our web site at http://www.arrays.ucsf.edu/software/.

Best,

Agnes


-----Original Message-----
From: Rob J Goedman [mailto:goedman at mac.com]
Sent: Sat 5/28/2005 8:13 AM
To: bioconductor at stat.math.ethz.ch
Cc: Paquet, Agnes
Subject: maQualityPlots (qpHexbin) question
 
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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