Cloned repo for MA analysis via the probeset list

adjusted so that data will be read properly
Changed loading to work using probeset data

I want to use the blast hits to the probes to select
mitochondrial contigs rather than simply blasting
the whole contig to try and get a more accurate idea
of mitochondrial expression by using probes that
contain mitochondrial sequences.

None of the probes are perfect hits, at some point I
 will need to decide on a cut off point
Made mito_probes' header more accurate
Adjusted 2_clean.R for Array probeset data input

The rest should work fine now
Attached gene name to contigs via probe
Adjust report to make it sense-y
Correcting table

Not yet finished making it print but am some of the way there
Finished correcting table!

Problem was a wrong variable name
Correction to filter set selection

I'd messed with the filter set selection so the
thresholds were wrong
Adjusted report because Tidal filter works right
Made names of table more sense-y
Adjusted line graph colours

Trying to find a nice selection of colours for
datasets with more than 12 qualitative classes
playing with colour some more

this is using the hcl rainbow to find colours - they aren't distinct enough for me really
More colour playing

using the I want hue tool to generate random palettes
of specific size - useful tool.
Errant bracket
Added a readme
Prepare for merge into Old_microarray_analysis
Merge branch 'master' of /Users/oj/Documents/Dropbox/R/Array_probeset_analysis

Conflicts:
	1.5_functions.R
	3_functions.R
	Array_probeset_analysis/1.5_functions.R
	Array_probeset_analysis/2_clean.R
	Array_probeset_analysis/3_functions.R
	Array_probeset_analysis/4_do.R
	Array_probeset_analysis/report.Rnw
	microarray_analysis/1.5_functions.R
	microarray_analysis/3_functions.R
	microarray_analysis/5_report.Rnw
	report.Rnw