11 protocols
AccessionType
image_aquisition
Standard Agilent protocol.
bioassay_data_transformation
ID_REF = VALUE = Normalized and log2-transformed ratio (test/reference)
feature_extraction
Median normalization in R/Bioconductor. Raw data files: Test: Cy3 sample in the ''US22502676_252252210311_S01_CGH_105_Dec08_1_2.txt file. Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.
feature_extraction
Median normalization in R/Bioconductor. Raw data files: Test: Cy5 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_2.txt' file. Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.
feature_extraction
Median normalization in R/Bioconductor. Raw data files: Test: Cy5 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file. Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.
feature_extraction
Median normalization in R/Bioconductor. Raw data files: Test: Cy5 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_3.txt' file. Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.
nucleic_acid_extraction
DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al., J Pathol. 2007 Jan;211(1):45-51 (PMID 17117405).
hybridization
Standard Agilent protocol.
labeling
DNA labeling protocol according to Enzo Life Sciences.
feature_extraction
Median normalization in R/Bioconductor. Raw data files: Test: Cy3 sample in the ''US22502676_252252210311_S01_CGH_105_Dec08_1_1 file. Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.
feature_extraction
Median normalization in R/Bioconductor. Raw data files: Test: Cy3 sample in the ''US22502676_252252210311_S01_CGH_105_Dec08_1_3.txt file. Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.