Answer to Question #154929 in Bioinformatics for vaibhav

Question #154929

(a) A researcher is scanning a cDNA microarray and obtains an image with the following characteristics: most of the spots are visible and many are very bright; the background appears to be light gray. The researcher proceeds to the image processing and quantification stages and finds that most spots appear to be characterized by a high average intensity. Discuss what might have happened? What steps would you undertake in order to test your hypothesis and correct the situation?

(b) What experiment can be used as an alternative to microarray analysis? What are its advantages over the former?

(c) What is the difference between concordant, discordant and unmapped reads?

Expert's answer

a)Derease the variability--of low-intensity spot values. In contrast,seeded region growing segmentation with morphological background correction provides precise and accurate estimates of foreground and background intensities

b) mRna-Sequence

It offers improved specificity, so it's better at detecting transcripts, and specifically isoforms, than microarrays. It's also more sensitive in detecting differential expression and offers increased dynamic range.

c) Concordant pairs match pair expectations, discordant pairs don't while unmapped reads map nowhere on the reference genome.

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