Midterm 1 Solutions

0001/01/01

Question 1.

I think that lecture 01 sufficiently covers the different concepts and you received significant marks if you acknowledged some of the central issues discussed there.

I did remove marks if there wasn’t care taken to discuss security and address the fact that Cloud solutions are likely not possible with clinical samples (unless extreme care is given either through cryptography or through special types of cloud computing). This aspect of the question builds on Question 1 of assignment 1 that asked you to investigate what rights Google reserves when data is stored on their server.

Question 2.

I was happy if you tried to cover the three main characteristics of modern computing and had reasonable arguments for or against. I tried to point out some statements that might be a bit problematic (eg they only deal in plastic - but computer only deal in electrons). An important aspect here is that there is a computer that programs the 3D printer; that is seperate from the printer itself.

Question 3.

Straightforward.

Question 4.

4e.

small_brca %>% filter( FOXC1 > 245 ) %>% count

4f.

 bw <- small_brca %>% filter( gender=="FEMALE", tumor == TRUE, race == "BLACK OR AFRICAN AMERCICAN")

4g.

 small_brca %>% select( participant, vital_status, ANLN:TMEM45B, -RRM2)

4h.

small_brca %>% mutate( triplenegative = ((er_status_by_ihc == "Positive") & !(her2_fish_status=="Positive")))

ggplot(data = small_brca) +  
geom_point(mapping = aes(x = GRB7, y = EGFR, color=tumor)) + 
facet_wrap(~ tumor_status, nrow = 2) +
scale_y_continuous(trans='log')   + scale_x_continuous(trans='log') + 
ggtitle("GRB7 and EGFR expression by tumor_status") +
xlab("log GRB7 expression") +  ylab("log EGFR expression")

6a.

tmp <- small_brca %>% filter( gender=="FEMALE" ) %>%
        distinct(  ) %>%                     # I would have also been happy with filter( tumor==FALSE ) as a surrogate.
        drop_na( )  %>%  
        summarise(m = mean(as.numeric(age_at_diagnosis)))      
        # I didn't remove grades if drop_na wasn't here.

6b. I will leave these open as Quiz 2 covers question b and it is good practice for you to get right.