Preprocessing for TCGA RPPA Data - GBM

[Archana Ramesh]

Hello,

My name is Archana. I am a graduate student at Arizona State
University using some of the TCGA GBM data for my research. I am
specifically interested in the RPPA data available on your portal.
Could you please let me know what kind of preprocessing has been done
on this data ?

Thanks,

Archana Ramesh
http://www.public.asu.edu/~aramesh2/

[Jianjiong Gao]

Hi Archana,

The RPPA data in the portal were from MD Anderson Cancer Center. Below
were the data processing steps:

1) Tumor or cell lysates were two-fold-serial diluted for 5 dilutions
(from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated
slide in 11x11 format.
2) Samples were probed with antibodies by CSA amplification approach
and visualized by DAB colorimetric reaction.
3) Slides were scanned on a flatbed scanner to produce 16-bit tiff image.
4) Spots from tiff images were identified and the density was
quantified by MicroVigene.
5) Relative protein levels for each sample were determined by
interpolation of each dilution curves from the "standard curve"
(supercurve) of the slide (antibody). Supercurve is constructed by a
script in R written by Bioinformatics. These values (given as Log2
values) are defined as Supercurve Log2 value".
6) All the data points were normalized for protein loading and
transformed to linear value designated as "Linear after
normalization".
The linear value can be used for "bar graph" or further analysis
according to your study design.
7) "Linear after normalization" value was transformed to Log (natural)
value and median centered value.
8) We integrated the median centered values into our portal.

You could also find some more information on MD Anderson website:
http://goo.gl/faCw7

I hope this helps. Please feel free to contact us to any further questions.

Best regards,
-Jianjiong

Jianjiong Gao, PhD
cBio, MSKCC