From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001 From: Bonface Date: Fri, 9 Feb 2024 09:41:28 -0600 Subject: Update dataset RTF Files. --- general/datasets/BRF2_M_0304_P/notes.rtf | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 general/datasets/BRF2_M_0304_P/notes.rtf (limited to 'general/datasets/BRF2_M_0304_P/notes.rtf') diff --git a/general/datasets/BRF2_M_0304_P/notes.rtf b/general/datasets/BRF2_M_0304_P/notes.rtf new file mode 100644 index 0000000..c4a728d --- /dev/null +++ b/general/datasets/BRF2_M_0304_P/notes.rtf @@ -0,0 +1,5 @@ +

Data were processed using the Microarray Suite 5 (MAS 5) 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.

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Data were processed using the Position-Dependent Nearest Neighbor (PDNN) method developed by Zhang and colleagues (2003. 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.

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Data were processed using the RMA 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.

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