On Wed, Oct 24, 2012 at 4:45 AM, priya [guest] <guest@bioconductor.org>wrote:

>
> ID_REF           GSM133971          GSM133972               GSM13397
> 244901_at   5.95461158752441E+001   1.88836498260498E+001   1.9821
> 244902_at   7.25400314331055E+001   2.65250205993652E+001   1.9532
> 244903_at   2.23291015625000E+002   1.78133636474609E+002   5.3816
> 244904_at   3.65505447387695E+001   3.04016351699829E+000   6.8046
> 244905_at   4.07523269653320E+001   2.58869285583496E+001   1.1808
> 244906_at   1.50184860229492E+002   5.39840278625488E+001   4.1491
> 244907_at   2.65190029144287E+001   1.39808797836304E+000   2.0866
> 244908_at   3.50156021118164E+000   1.05003893375397E+000   4.5765
>
>
>  -- output of sessionInfo():
>
> In the above dataset the first two columns are MAS5.0 normalized and the
> last column is RMA normalized. Would it be be possible to denormalize the
> dataset so that I can perform RMA normaliztion throughout ?


No, that is not possible.  However, these look to be data from NCBI GEO.
 Have you checked to see if the .CEL files are available?  I suspect that
they are.  You could use GEOquery to download the .CEL files (or do it
manually if you like) and then perform RMA normalization on the original
.CEL files.  Note, though, that your analysis results may not be easily
interpretable if you are mixing data from different experiments due to
batch effects.

Sean


> The last column was from a different experiment which I needed to append.
> SO the normaliztions are different.
>
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