[BioC] FW: Bioconductor

[Dana.Stanley at csiro.au]

Dear All


As you can probably see below, I have been trying to learn Bioconductor for a while now. I asked a number of researches that do microarray analysis about it and only few were using it but nobody was quite skilled with it. 
I contacted Bioinformatics Department at WEHI Melbourne where Dr Smyth and other contributors are situated to ask if there are any workshops in Melbourne but there was nothing happening. I purchased Use R books on Bioconductor and stared by learning basic R so I can do basic stats on R now but I never achieved much on Bioconductor by myself. My biggest issue is that there are not many people that are skilled with it, and the ones that are have no time for beginners like myself. It would be great if you had dedicated book that can lead a beginner from step one onwards. The pdf-s provided for different packages are suitable for users skilled in  Bioconductor. For example oligo package I am trying to learn is going through the example dataset in their pdf document. This does not help me to upload my data let alone anything more. There is no detailed explanation of arguments with examples or maybe analysis pipeline starting from how to prepare your data for upload, in which folder (I suppose workdir) to put it and how to upload and inspect etc. 
I learned some R thanks to YouTUBE videos. I tried through the books, and I find R books (pdf from the R website) quite good, but the videos I watched helped me beyond the words. Is there anything like that for bioconductor? I looked for lessons (private or online) for Bioconductor, I am willing to pay for it, but without success. 
Is there anything you could suggest?

Thanks


Dana












-----Original Message-----
From: Vincent Carey [mailto:stvjc at channing.harvard.edu] 
Sent: Tuesday, 16 March 2010 10:30 PM
To: Stanley, Dana (LI, Geelong AAHL)
Subject: Re: Bioconductor

write a detailed email to bioconductor at stat.math.ethz.ch, following
the posting guide on the web site, describing your encounter with the
deficiencies of bioconductor.  the project can only benefit from data
on your experience, provided you describe it with care.  nimblegen
arrays are not a primary tool for the core developers so the pedagogic
material is not as carefully developed for nimblegen as it is for,
e.g., affy or illumina.  remember, neither you nor nimblegen are
paying the project in any way for anything.

On Tue, Mar 16, 2010 at 1:58 AM,  <Dana.Stanley at csiro.au> wrote:
> Hi All
>
>
>
> I am desperately trying to learn Bioconductor by myself and it is just
> driving me crazy. I learned basic R and I am able to import text files and
> do some stats and graphs. I am using Nimblegen arrays and my first attempt
> to use oligo package was total disaster. I find the manuals very hard to
> follow. They do not tell you basic things like how to upload data (my own
> data). The pdf on analysis of Nimbeegen dataset (by Carvalho) does not
> explain much on how to import my own data, where to put my xys files, how to
> read them into the R etc.
>
> My today's Bioconductor session has already ended in tears. I looked for
> Bioconductor help by looking up researches that use it, I tried to get
> someone to give me just one lesson, I bought all the R project books I could
> find.
>
>
>
> Is there anything else I could try before I give up?
>
> Is there avi screen capture demo around?
>
>
>
> Thanks
>
>
>
> Dana
>
>
>
> Dana Stanley B.Eng (Pharmaceutical), PhD Molecular Biology
> Postdoctoral Fellow
>
> CSIRO Livestock Industries
>
> Australian Animal Health Laboratories
>
> Private Bag 24, Geelong,
>
> Victoria 3220, Australia
>
>
>
> Phone: +61 3 5227 5628
>
> Fax:     +61 3 5227 5555
>
>