On Sun, Aug 9, 2009 at 6:48 PM, Peng Yu <pengyu.ut@gmail.com> wrote:

> On Sun, Aug 9, 2009 at 4:46 PM, Kasper Daniel
> Hansen<khansen@stat.berkeley.edu> wrote:
> >
> > On Aug 9, 2009, at 13:06 , Peng Yu wrote:
> >
> >> On Sun, Aug 9, 2009 at 12:03 PM, Sean Davis<seandavi@gmail.com> wrote:
> >>>
> >>> Hi, Peng.
> >>>
> >>> I don't mean to sound rude, but everyone on this list is quite busy.
>  You
> >>> will need to make time to do some of your own research, unfortunately.
> >>>  As
> >>> an exercise and an answer to your question, check out the Table of
> >>> Contents
> >>> of the R Data Import/Export.  If there is still a question about what
> >>> section is most appropriate, feel free to post back to the list the
> code
> >>> you
> >>> have tried, any error messages, and the output of sessionInfo().  And,
> >>> yes,
> >>> you will benefit from at least skimming the entire manual--you will
> learn
> >>> quite a bit.
> >>
> >> Hi Sean,
> >>
> >> I have been skimming the manual. One thing I am not sure is that
> >> whether I should spend a few days on learning all the materials you
> >> mentioned, while I could use some other language that I am more
> >> familiar with and solve the problem quickly. I would like to solve my
> >> question today if possible. However, I completely understand that I
> >> should read all the manuals that you mentioned in the long run.
> >>
> >> I have thought of using perl to solve my problem. But I think that it
> >> is still better to figure out a way to do so in R as well. The code in
> >> perl would not be long, so I think the code in R would not be long,
> >> either. It doesn't seem that it would take an experienced R user a
> >> long time to figure out the R commands to map all the probeset_id to
> >> gene names or ensembl ids, does it?
> >>
> >> I know that I could use
> >> read.csv("MoGene-1_0-st-v1.na29.mm9.probeset.csv") to read the file,
> >> which gives a data frame. But how to extract the useful columns from
> >> the data frame? How to construct a mapping between the entry in one
> >> column to the entry in another column? I should use
> >> read.table("genes.txt") to read "genes.txt", right? How to replace its
> >> first column with the appropriate gene names or emsembl id using the
> >> mapping?
> >>
> >> It seems that MoGene-1_0-st-v1.na29.mm9.probeset.csv should have
> >> enough annotation information for my problem. Why do I need
> >> "mogene10stprobeset.db"?
> >
> > Peng,
> >
> > Let me quote Wolfgang Huber: "the purpose of this mailing list is not for
> > other people to do your homework for you".  I don't think anyone are very
> > inclined to help you, if you don't spend some time yourself reading about
> > the language.  Some of the questions you ask above are stuff you ought to
> > know after spending 10 minutes with "An introduction to R".
> >
> > I believe in using the right tools for the job, and if you think you can
> do
> > your stuff in a few hours using Perl, I think you should use Perl.  If
> you
> > want access to some of the powers and time saving features of R, you need
> to
> > devote some time to learning it.  But you cannot expect to do even simple
> > stuff in a new language without spending some initial time on it.
>
> Hi Kasper
>
> I don't think that I want somebody to do the homework for me. One
> thing that I feel frustrated about reading R documentation is that the
> useful information is often scattered in different places, which is
> not easy for a new user to piece them together. One example is
> mogene10stprobeset.db, whose document doesn't mention AnnotationDbi. I
> feel that learning from example complementing with reading R
> documentation is a more efficient way.
>

We can agree that documentation can always be improved.  That said, the
documentation that exists is generally good and worthy of attention.  If
there are shortcomings in the documentation, please let us know, as we can
try to improve the project based on constructive feedback.

>
> BTW, Do you know why "mogene10stprobeset.db" is needed if I have
> MoGene-1_0-st-v1.na29.mm9.probeset.csv already?
>

The .csv file has most of the information, yes.  However, as the
AnnotationDbi vignette shows, there are some advantages to using the .db
annotation packages.  In particular, the .db packages have not only data but
methods for dealing with the data rather efficiently and quickly and the
data are both self-describing and standardized between annotation packages.


Sean

	[[alternative HTML version deleted]]

