Selection of gene expression analysis and data mining software

[Eric Flores]

I'm being asked to select two (2) gene expression software packages
for use during my semester course in DM for Genomics and Proteomics. I
have already chosen to use Bioconductor as the first package because
there is a lot documentation out there for using it. It seems to
implement many methods and being mature enough to manage almost
anything of what we could find in my course. Being open source was the
other key important reason. Per instance, the academic version of
Array Studio is $1500, which is ridiculous as very few students would
be able to afford it.

I was looking at selecting dChip for the second package. It seems to
be well documented and easy to use. However, I'm might not be aware
about other worthy candidates out there. Also, since I'm just learning
to use them, I'm not as qualified as this community to evaluate the
feature set of the available packages. I know that we will do Feature
Selection in the next project, but beyond that, I would like to select
a package which serves as a good complement to Bioconductor (I already
found documentation about Feature Selection in Bioconductor). I think
about a package that, while not as extensive as Bioconductor, is
easier to use.

It would be awesome if provides features to verify results obtained
with Bioconductor (while not necessarily having eveyrthing).

Feel free to suggest other packages if you believe that they are
better candidates for the intended use. However, be aware that because
of restrictions placed by the professor they cannot be any of the
following (sorry):

BRB ArrayTools
Expression Profiler
GEDA / caGEDA
GeneMaths
GenePattern
Genes@Work
GeneSpring GX
GEPAS / Babelomics
MeV (MultiExperiment Viewer)

Thanks a lot!

[simon]

Hi all and Cheng,
For some reason, we have to dig out old expression chip HG U95A. When
I opened group but quickly get error message , please see below.
Anybody have similar experience and your feedback will be appreciated.
Thanks
Simon

{Open group expression
Treat this array type as 'Expression'
Reading in existing binary CDF file
G:\Mclean\research\geneexp\HG_U95A\HG_U95A.CDF.bin (file format 4)...

Search and extract 'CEL' probe data files of chip type 'HG_U95A' in
'G:\Mclean\research\geneexp'...

Found 1: G:\Mclean\research\geneexp\11111b.CEL
Treat this array type as 'Expression'
Reading in existing binary CDF file
G:\Mclean\research\geneexp\HG_U95A\HG_U95A.CDF.bin (file format 4)...

Reading CEL file...
Not a text format CEL file, use binary reading
CEL rows: 712, CEL cols: 712, CDF dim: 640
Opening group not completed}

{Group expression is closed}