Hi everyone,
I've been playing with the hsahomology package and gone through the
vignette and there is something I don't understand.
Sometimes it seems the scores are in homoURL instead of homoPS. It
seems
like a bug to me, or is it a feature I don't understand?
> homo <- unlist(as.list(hsahomologyDATA))
#one arbitrary case where this is the case
> x<-grep("396050", homo)
> as.matrix(homo[(x-2):(x+2)])
[,1]
6337.9031.homoOrg "gga"
6337.9031.homoType "m"
6337.9031.homoHGID "396050"
6337.9031.homoPS NA
6337.9031.homoURL "66.84"
There seems to be a lot of cases where this happens, and it would seem
to me that most of the code using those scores would be rather
confused
by this.
> sessionInfo()
R version 2.4.0 Patched (2006-10-03 r39576)
i386-apple-darwin8.8.1
locale:
C
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils"
"datasets"
[7] "base"
other attached packages:
hsahomology
"1.14.0"
Francois
Hi, Francois,
> Sometimes it seems the scores are in homoURL instead of homoPS. It
seems
> like a bug to me, or is it a feature I don't understand?
Yes, it is a bug. Thanks for the report.
>
> > homo <- unlist(as.list(hsahomologyDATA))
> #one arbitrary case where this is the case
> > x<-grep("396050", homo)
> > as.matrix(homo[(x-2):(x+2)])
> [,1]
> 6337.9031.homoOrg "gga"
> 6337.9031.homoType "m"
> 6337.9031.homoHGID "396050"
> 6337.9031.homoPS NA
> 6337.9031.homoURL "66.84"
>
> There seems to be a lot of cases where this happens,
I can bet that you see the problem when and only when homoType=="m".
Anyway, I have updated all the
homology data packages (30 of them) in bioc 2.0 repository. The source
packages and windows binaries
in bioc 1.9 should be available before the end of the day. You will
get something in "homoURL" only
when homoType == "c" and in that case homoPS will be NA. In all other
cases, "homoURL" will always
be NA. In hsahomology, homoType can only be "m", "B" or "b", i.e.
homoURL is always NA.
> and it would seem
> to me that most of the code using those scores would be rather
confused
> by this.
Hope those codes are not confused any more. Now, seriously, do you
know any packages that use those
scores? I am curious about this because the source data that we used
to generate hsahomology will be
deprecated in Jan, 2007. It is not easy to get those scores from the
new data format. So, I am
curious how heavily this data is being used. Thanks.
nianhua
Hi Nianhua,
> Hope those codes are not confused any more. Now, seriously, do you
know any packages that use those
> scores? I am curious about this because the source data that we used
to generate hsahomology will be
> deprecated in Jan, 2007. It is not easy to get those scores from the
new data format. So, I am
> curious how heavily this data is being used.
I don't know of any package that use it. I just wanted a quick and
dirty
way to convert gene list across species and started playing around
with
those packages.
The vignette worked properly but if I deviated slightly then I got
those
strange results.
If I'm the first person to realize this, I would think that not many
people are using them.
Francois
Nianhua Li <nli at="" fhcrc.org=""> writes:
> I can bet that you see the problem when and only when
> homoType=="m". Anyway, I have updated all the homology data packages
> (30 of them) in bioc 2.0 repository. The source packages and windows
> binaries in bioc 1.9 should be available before the end of the
> day.
Thanks, Nianhua, for the prompt fixes :-)
> Hope those codes are not confused any more. Now, seriously, do you
> know any packages that use those scores? I am curious about this
> because the source data that we used to generate hsahomology will be
> deprecated in Jan, 2007.
As I understand it, the data is already deprecated and in Jan 2007 it
will be _defunct_, that is, no longer available.
> It is not easy to get those scores from the new data format. So, I
> am curious how heavily this data is being used. Thanks.
Yes, it would be nice to access how useful these are before putting a
lot of resources towards building them :-)
+ seth
