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| author | Bonface | 2024-02-13 23:52:26 -0600 |
|---|---|---|
| committer | Munyoki Kilyungi | 2024-08-09 13:30:43 +0300 |
| commit | b2feda451ccfbeaed02dce9088d6dd228cf15861 (patch) | |
| tree | 3dd2883524985114070a7770cd2e9f9bd7eb1848 /general/datasets/Brf2_m_0304_r/notes.rtf | |
| parent | d029d5d7f8ead1f1de8d318045004a4a6f68f5fb (diff) | |
| download | gn-docs-b2feda451ccfbeaed02dce9088d6dd228cf15861.tar.gz | |
Update dataset RTF Files.
Diffstat (limited to 'general/datasets/Brf2_m_0304_r/notes.rtf')
| -rw-r--r-- | general/datasets/Brf2_m_0304_r/notes.rtf | 5 |
1 files changed, 5 insertions, 0 deletions
diff --git a/general/datasets/Brf2_m_0304_r/notes.rtf b/general/datasets/Brf2_m_0304_r/notes.rtf new file mode 100644 index 0000000..c4a728d --- /dev/null +++ b/general/datasets/Brf2_m_0304_r/notes.rtf @@ -0,0 +1,5 @@ +<p>Data were processed using the Microarray Suite 5 (<a class="normal" href="www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf">MAS 5</a>) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.</p>
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+<p>Data were processed using the Position-Dependent Nearest Neighbor (<a class="normal" href="http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/" target="_blank">PDNN</a>) method developed by Zhang and colleagues (<a class="normal" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12794640" target="_blank">2003</a>. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with careful consideration to balancing samples by sex, age, and environment.</p>
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+<p>Data were processed using the <a class="normal" href="http://stat-www.berkeley.edu/users/bolstad/RMAExpress/RMAExpress.html" target="_blank">RMA</a> protocol and are presented with secondary normalization to an average expression value of 8 units. To simplify comparison between transforms, RMA values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with effort to balance samples by sex, age, and environment.</p>
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