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Aakanksha
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Our group needs a section of a programming assignment to be completed this weekend as its due Feb 1 2010. The programming language is mathlab.

The working program is attached to this message.

Questions are below:

Our group needs a section of a programming assignment to be completed this weekend as its due Feb 1 2010. The programming language is mathlab.

Questions are below:

b- Plot the mean and standard deviation for each sample. Identify the 2 sets of outliers whose statistics are different to the rest, print the sample ids and remove those samples from the data.

d- Plot the histogram for the minimum pairwise Pearson correlation between markers. If we set a reasonable threshold, such as 0.7, what is the number of genes above the threshold? How many below the threshold?

f- Modify the code to filter out all markers whose standard deviation is lower than

0.25. How many genes are filtered in now?

g- Look at gene RALGAPA1 (Entrez id 253959) using printInfoForGene. In this case there is one probe with completely different behavior without having low standard deviation. Could you give a plausible reason for the behavior of this marker?

h- BAX (Entrez id 581) and Rb1 (Entrez id 5925) are key genes in cancer (RB1 is especially well known in Glioblastoma). However those genes have been filtered out. Use printInfoForGene to visualize the data for those genes. You should see two clear clusters for each gene. Find another two examples that show this behavior and propose a biological explanation for the phenomenon.

k- Your current code does not normalize the values for the markers before calculating the gene expression as the average across them. Explain why the code should or should not normalize these values. Note: suppose the normalization is performed just before taking the mean, it is, it does not affect the decision of which markers are selected or whether the gene should be filtered out.

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