[BioC] How do you keep track of your analyses

[Michal Blazejczyk]

Hi Ali,

If you permit a little bit of self-promotion...  You may want to look
at FlexArray, a Windows application we developed that is a thick
wrapper around Bioconductor to do statistical data analysis on
expression microarray results:
  http://genomequebec.mcgill.ca/FlexArray/
FlexArray will not handle huge projects or very complex analyses,
but it performs quite well on small- to mid-sized Affy and Illumina
gene expression projects.  And it is extensible (algorithm plug-ins).

One of our guiding principles has been to keep track of everything
that is done during an analysis: input data, output data, parameters,
R code executed...  So you can always go back, review your past
analysis steps, or export an analysis as a "protocol", and then
apply it to new data, after tweaking some parameters if you wish.

Best regards,

Michal Blazejczyk
FlexArray Lead Developer
McGill University and Genome Quebec Innovation Centre
740, Dr Penfield Avenue
Montreal (Quebec) Canada H3A 1A4
Phone: 514-398-5187
E-mail: flexarray at genomequebec.ca
Internet: genomequebec.mcgill.ca/FlexArray


> Hello,
>
> I am doing an increasing number of bioconductor analyses for various
> people and I am starting to find it difficult to keep track of what I
> have done previously.  A common question six months after the initial
> analysis is something like "Can you do the same as x but change y".
> Has anyone got any idea on the best way to do this.
>
> The essential components to keep track of are:
> * input files
> * R code used
> * output files
> * Description of what you aim to do.
>
> The two possibilities that I can think of is:
> 1) Some structured directories e.g.
> ProjectName_Person
>         /Description.txt
>         /Analysis1_date
>                 /InputFiles
>                 /Rcode
>                 /Output/Outputfiles
>
> 2) Some sort of personal wiki like TiddlyWiki
>
> Its got to be searchable in some form too.
>
> Any experiences in this realm?
>
> Many thanks
>