[BioC] can't instal MetaData package "mouse4302"

[Gordon Smyth]

At 01:11 PM 12/03/2005, Seth Falcon wrote:
>Hi Gordon,
>
>The mouse4302 annotation package is again available.  The version is
>1.6.9.  The data is the same as version 1.6.8, the packaging was
>modified so that the package is usable on Windows.
>
>Sorry for the delay.
>Best,
>+ seth

Hi Seth,

Many thanks for this.  I'll update my recent Mouse 430 2.0 analyses with 
this package.

I've compared versions 1.6.5 and 1.6.9 of the mouse4302 annotation package 
and found somewhat more differences than I expected.  3758 probe sets have 
symbols now which didn't before, and 166 probe sets which previously had 
symbols have no symbol now.  More surprisingly, a further 3940 probe sets 
have different symbols than before.  That makes 7864 probe sets in total 
for which the gene symbols have changed.

Are these changes just a reflection of changes in the public databases, or 
have there also been changes in how the content of the annotation package 
is assembled?  It seems that there have.

Many of the changes from version 1.6.5 to 1.6.9 look like improvements, but 
there are also some which seem clearly wrong.  For example, consider probe 
set 1460164_at.  This probe set is identified by NETAFFX as being gene 
"Spin" with LocusLinkID 20729, and that was the information given in 
version 1.6.5 of the mouse4302 package.  In version 1.6.9, this probe set 
has been re-assigned to LocusLink 102420 which, according to Entrez Gene, 
is an obsolete identifier.  What information is being used by the package 
builder which could cause the LocusLinkID given by Affymetrix to be over-ruled?

Many thanks for your help
Gordon

 > library("mouse4302")
 > packageDescription("mouse4302")$Version
[1] "1.6.5"
 > packageDescription("mouse4302")$Created
[1] "Thu Oct 21 16:13:45 2004"
 > mouse4302.v165 <- as.list(mouse4302SYMBOL)
 > detach(2)
 > library(reposTools)
 > install.packages2("mouse4302")
Note: You did not specify a download type.  Using a default value of: Win32
This will be fine for almost all users

[1] "Attempting to download mouse4302 from 
http://www.bioconductor.org/data/metaData/"
[1] "Download complete."
[1] "Installing mouse4302"
[1] "Installation complete"
 From URL:  http://www.bioconductor.org/data/metaData/
         mouse4302 version 1.6.9

 > library("mouse4302")
 > packageDescription("mouse4302")$Version
[1] "1.6.9"
 > packageDescription("mouse4302")$Created
[1] "Fri Mar 11 13:54:41 PST 2005"
 > mouse4302.v169 <- as.list(mouse4302SYMBOL)
 > o165 <- order(names(mouse4302.v165))
 > o169 <- order(names(mouse4302.v169))
 > mouse4302.v165.symbol <- unlist(mouse4302.v165)[o165]
 > mouse4302.v169.symbol <- unlist(mouse4302.v169)[o169]
 > table(v165=is.na(mouse4302.v165.symbol),v169=is.na(mouse4302.v169.symbol))
        v169
v165    FALSE TRUE
   FALSE 36489   166
   TRUE   3758  4688
 > notna <- !is.na(mouse4302.v165.symbol) & !is.na(mouse4302.v169.symbol)
 > noteq <- (mouse4302.v165.symbol[notna] != mouse4302.v169.symbol[notna])
 > sum(noteq)
[1] 3940
 > tab.noteq <- 
data.frame(v165=mouse4302.v165.symbol[notna][noteq],v169=mouse4302.v169.symbol[notna][noteq])
 > tab.noteq[1:20,]
                       v165          v169
1415692_s_at          Canx      AI316784
1415693_at   1110021N07Rik         Derl1
1415703_at           Ureb1 C430014N20Rik
1415711_at   D130059B05Rik       Arfgef1
1415712_at          Zranb1         Ctbp2
1415715_at            Slbp 2410015J15Rik
1415719_s_at          Arcp         Armc1
1415720_s_at 2510031P20Rik      Mad2l1bp
1415725_at   E130302O19Rik          Rrn3
1415726_at        BC038311      AU017193
1415758_at   2510002A14Rik 2010313D22Rik
1415765_at           Bscl2      AI465155
1415793_at        AI415282          Pnpo
1415937_s_at       Pdcd6ip      AI197427
1415948_at          Pappa2         Creg1
1415953_s_at         Mark2      AU024026
1415954_at            Try4 1810049H19Rik
1416043_at            Nasp A430091L06Rik
1416046_a_at 0610025O11Rik         Fuca2
1416047_at   0610025O11Rik         Fuca2
 > library(annotate)
 > getSYMBOL("1460164_at",data="mouse4302")
[1] NA
 > getLL("1460164_at",data="mouse4302")
[1] 102420
 > version
          _
platform i386-pc-mingw32
arch     i386
os       mingw32
system   i386, mingw32
status
major    2
minor    0.1
year     2004
month    11
day      15
language R