Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

Appendix C
# Sample analysis from Cleansin_Graphics_7_23.py after visual batch inspection (Graphic,
Graphic_nobatch, or Graphic_MSR (raw data) functions in same file)
def Driver(usr, pswd, db, gfiles, logfile):
Cel_Probe_Filter(usr, pswd, db, gfiles[0], logfile)
Cel_Probeset_Filter(usr, pswd, db, gfiles[1], logfile)
def Cel_Probe_Filter(usr, pswd, db, gfile, logfile):
cur, conn= make_connect(usr, pswd, db)
msk, Lmsk, state=get_inc_mask(cur)
cc=zeros(len(Lmsk))
states=get_unique_states(cur)
for i in range(len(state)):
cc[i]=states.index(state[i])
r.pdf(gfile, height=11, width=8)
r.par(mfrow=r.c(2,1))
fp=open(logfile,'a')
for i in range(len(states)):
ptr=nonzero(equal(i,cc))
mu, prbs = zeros(len(ptr), Float), zeros(len(ptr), Float)
x=range(len(ptr))
nbr=len(ptr)
k=0
for j in ptr:
tmp='select signalrawintensity from '+ msk[j]+'_sr4'
cur.execute(tmp)
rows=cur.fetchall()
prbs[k]=len(rows)
mu[k]=(sum(rows)[0])/prbs[k]
k+=1
# plot intensities
r.plot(x, mu, main='Intensity Filter ('+states[i]+')',
xlab='Array Number', ylab='Average Cel Intensity', pch=21, col='blue',
ylim=r.c(r.mean(mu)-(2.5*r.sd(mu)), r.mean(mu)+(2.5*r.sd(mu))))
# 2 std dev
r.lines(x, r.rep(r.mean(mu)-(2*r.sd(mu)), nbr),
col=r.rgb(227/256.,26/256.,28/256.), lty=3, lwd=1)
r.lines(x, r.rep(r.mean(mu)+(2*r.sd(mu)), nbr),
col=r.rgb(227/256.,26/256.,28/256.), lty=3, lwd=1)
# 1 std dev
r.lines(x, r.rep(r.mean(mu)-r.sd(mu), nbr),
col='turquoise', lty=4, lwd=1)
r.lines(x, r.rep(r.mean(mu)+r.sd(mu), nbr),
col='turquoise', lty=4, lwd=1)
# mean
r.lines(x, r.rep(r.mean(mu), nbr), lty=2, lwd=2)
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