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

[Robert Gentleman]

Hi Gordon,
   Thanks for the careful report - we will be looking in to this and see  
what can be resolved. Some issues are due to the move to Seattle  
(hopefully that is mostly resolved now), and some due to the change  
from LocusLink to EntrezGene - and that is more problematic as our  
basic data sources have changed completely.

   Best wishes,
     Robert

On Mar 11, 2005, at 10:40 PM, Gordon Smyth wrote:

> 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.symbo 
> l))
>        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
>
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
+----------------------------------------------------------------------- 
----------------+
| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
       |
| Fred Hutchinson Cancer Research Center                                 
          |
| email: rgentlem at fhcrc.org                                              
                          |
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