[OT] compatible preprocessing for Affy and non-Affy
0
0
Entering edit mode
@adaikalavan-ramasamy-675
Last seen 9.6 years ago
[[Apologies in advance since this may be an off topic subject but I have tried hard without finding any consensus.]] Problem: I am trying to combine data from Affymetrix platform and non-Affymetrix platform (most of them two-color technologies) from the raw data (e.g. CEL, GPR). Therefore I need to find the choice of "compatible" preprocessing for Affy and non-Affy. I found 3 studies trying to combine Affy with non-Affy. Irizarry et al (PMID:15846361) uses RMA for Affy and print-tip normalization with no background correction. Larkin et al (PMID:15846360) uses Li-Wong for Affy and LOWESS followed by z-scoring between array subgrids. I am unclear how Brammler et al (15846362) preprocessed their data (although one of the supplementary alludes to MAS 5.0 for Affymetrix). Therefore, I have decided to use RMA for Affy and LOESS normalisation followed by z-scoring (i.e. zero mean, unit variance) the columns/arrays for non-Affy platforms. Question: Can anyone kindly point me to any other papers that tries to address this question? Can anyone comment/correct me on my decision? Any other suggestions kindly welcome. Thank you. Regards, Adai
Normalization Preprocessing affy Normalization Preprocessing affy • 706 views
ADD COMMENT

Login before adding your answer.

Traffic: 732 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6