Craig Wilding - 2010-09-23

I know that this should be an MeV forum not MIDAS but I sent an email to the MIDAS help account and haven't had a response (only a couple of days ago but i'd like to get this sorted ASAP). My question was:

I have just started to use MIDAS (and MeV) for analysis of my Agilent gene expression data.
I have had a tutorial in using MIDAS and MeV and am very impressed thus far but I have a query concerning how to get my data through MIDAS in the correct format.
My data are from 2 treatments, with 5 biological replicates within each so I have 5 arrays. 3 of these arrays are treatment 1 labelled Cy3 and treatment 2 labelled Cy5 whilst the other 2 arrays are treatment 1 labelled Cy5 and treatment 2 labelled Cy3. So, they are not strict dye swaps involving the same sample but there are swapped dyes within the experiment. The 3 options for bringing in the files are

1) read single datafile
2) read flip dye data file pairs
3) read all files in a folder

None of these is strictly appropriate for a format such as this.
Can you help?

Just to confirm, the samples are from treatment A and treatment B and there were 5 separate RNA extractions from each. The arrays are:

Cy3     Cy5
A1      B1
A2      B2
A3      B3
B4      A4
B5      A5

With thanks for your help,