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

tmp="update sample_mask set exclude =
true, description = 'avg array probe numbers above 2 stdevs"+"' where
mask_id = '"+msk[ptr[j]]+"'"
cur.execute(tmp)
conn.commit()
fp.write('\n'+msk[ptr[j]]+'
excluded:\tprobe numbers above 2 stdevs')
conn.close()
r.dev_off()
fp.close()
def Cel_Probeset_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:
# probesets do have a minumum of 4 probes
tmp='select distinct(probeset_id) from '+
msk[j]+'_sr4'
cur.execute(tmp)
rows=cur.fetchall()
prbs[k]=len(rows)
ps_sgnl=zeros(len(rows), Float)
k2=0
for l in rows:
tmp= 'select signalrawintensity from '+
msk[j]+"_sr4 where probeset_id = '" +l[0]+ "'"
cur.execute(tmp)
sri=cur.fetchall()
ps_sgnl[k2]=(sum(sri)[0])/len(sri)
k2+=1
mu[k]=r.mean(ps_sgnl)
k+=1
r.plot(x, mu, main='Probeset Intensity Filter
('+states[i]+')', xlab='Array Number', ylab='Average Cel Probeset
Intensity', pch=21, col='blue', ylim=r.c(r.mean(mu)-(2.5*r.sd(mu)),
r.mean(mu)+(2.5*r.sd(mu))))
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