comparative inference procedure

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Comparative Inference Procedure The main objective of any exploratory microarray data analysis is to short list the differentially expressed genes in two or more known groups or classes. The classes may correspond to tissues (cells) that are at different stages in some  process, or in different pathological states or in different experimental conditions. Foll owing ar e some exampl es , wh ic h wi ll il lu st ra te what we me an by identification of differentially expressed genes. (a ) Sa mples are taken fr om 20 br ea st canc er pa tients, before and af te r a 16- week course of chemotherapy and analyzed using microarrys. We wish to identify the genes that are up-or-down regulated in breast cancer after chemotherapy. (b) In a si ngle channel mi ce 2 dat a, it i s of inte re st to ide nt if y the genes, which are over or under expressed in treatment group relative to the control group. (c ) In two - channe l E.c ol i dat a, our aim is to ide nt if y the di ff erenti al ly expressed genes in mutant strain as compared to wild strain. In all the 3 applic ati ons given abov e, we wi sh to ide nti fy the dif fer ent ial ly expressed genes and the three applications look similar. However, (a) and (c) are examples of paired data whereas (b) is an example of the data on two independent samples. Following is similar but more complex example: d. There are 4 types of small round blue cell tumors (SRBT) of childhood - neuroblastoma (NB), rhabdomyosarcoma (RMS), the Ewing family of tumors (EWS) and Burkitt lymphomas (BL). Sixty-three samples from these tumors, 12, 20, 23 and 8 in each of the groups respectively, have been hybridized using single channel cDNA microarrays. The aim is to identify genes that are differentially expressed in one or more groups. The data for this experiment are known as khan’s data. This data set which, is very interesting and useful data, will be used at a later stage. 1

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