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Sun, 28 Oct 2007
limma
27 October 2007: limma 2.13.1
- lmFit() now tries to guess whether a data matrix contains log-ratios
or log-intensities.
When the input data object is a matrix, it is not possible to know
for certain whether the data are log-ratios or log-intensities, and
so lmFit() did not set the component Amean in the MArrayLM output
object. lmFit() now sets Amean if the input data values are all
positive, because the data are almost certainly log-ratios in that
case.
weaver
Update maintainer email address for pkgDepTools and weaver
affy
(1.17.1) the verbose flag is more properly respected by rma() and justRMA() then before when it was not passed down to the C code. This addresses the bug referred to in this BioC mailing list question: http://article.gmane.org/gmane.science.biology.informatics.conductor/15344
pkgDepTools
Update maintainer email address for pkgDepTools and weaver
affyio
(1.7.4) Fix issue related to parsing CDF file probeset units which do not have MM probes when using the binary xda format. This refers to an issue described/illustrated in this mailing list message: https://stat.ethz.ch/pipermail/bioc-devel/2007-October/001403.html
fix for decode_UINT8_t which was incorrectly returning an uint16. This should not have any effect for users using AGCC/Generic Binary Format CEL files, but improves the general robustness of the core parsing code.