[BioC] variation in output -using gcrma: bg correction

[Sucheta Tripathy]

Dear Group

when I run background(using GCRMA) correction for  chips:

"10_1331.1I.R208L.CEL"  "9_C101.1F.R9F2L.CEL" and for chips
"10_1195.1E.R119U.CEL"  "9_C101.1F.R9F2L.CEL" keeping
9_C101.1F.R9F2L.CEL as constant, For both the runs I get slightly
different outputs for chip 9_C101.1F.R9F2L.CEL (Data below). This does not
happen when GSB.adjust is set to FALSE. Also we have noticed the variation
seem to get lesser when we try more chips together.Any reason why it
should be happening this way?

Many thanks

Sucheta

My code:
-------
  obj<-ReadAffy(filenames=file)
  tmp1<-bg.adjust.gcrma(obj,optical.correct=T,affinity.info=affinfo)
  outfile<-paste(outdir, celfile[i,1], "_bg.txt", sep="")
  write.table(pm(tmp1), file=outfile, row.names=FALSE, col.names=TRUE,
sep="\t")
----------------------------------------------------------------------


"10_1331.1I.R208L.CEL"  "9_C101.1F.R9F2L.CEL"
---------------------------------------------
12.5854077145271    4.27009199115734
135.577788495271    115.177321956904
113.171763014501    124.781182045557
2.69508615100678    13.3527712251500
14.5462397159524    36.7662738574386
94.6480456343775    48.972931999473
230.750229599019    212.534925776574
242.058765502072    337.251490520153
233.871977591185    339.413283090951
134.355125363486    108.047618775561
136.685235380017    126.239703801863
76.2625488684543    45.3623158856175
148.251139760089    120.315265011794
328.121529159736    319.366509787047
291.865380794849    361.992073209429
3.97218796139000    4.20902848830535
14.6419514021341    31.6450267847893
28.8699339528603    67.3237575282198
110.496037483661    111.806067290232
22.2876523362755    41.5481196151883
205.194483921088    276.995029856902
84.8559677803056    96.0077121491932
778.222646971625    559.863168099135
4.83202857118797    11.3149613102092
3.66166154528273    39.6717762417948
67.7761672656053    94.6394189279102
112.500673213605    190.985739398352
171.007645212454    200.035151512867
492.236603432973    352.584270678829
130.800353580651    155.324195356517
146.303381286542    160.442554666605
4.34069757710996    61.4777011118527
88.9169964732945    84.2320613854983
69.1622655457769    60.1255829409642
382.758342400691    429.238548268896
3.90087434250685    4.02923006445781
245.047319536046    186.199916603738
4.60503013970163    16.7179032017834
45.8974167676779    58.6091870023334
152.737507677336    87.4646339988696
===================================================

"10_1195.1E.R119U.CEL"  "9_C101.1F.R9F2L.CEL"
---------------------------------------------
34.9453663026134    4.35753552341506
120.903734762231    116.962904914229
111.293345773408    133.421207928372
2.96910233809292    14.4050686356057
34.7269027797637    35.8835240852081
85.3109066158579    45.2284068764267
222.081465596656    201.346914814921
378.991271676870    336.282180468649
324.355847430672    337.586327159885
148.252162519851    107.763579952789
146.760939437243    127.027138121574
68.9112298899552    45.5584187250637
178.300028533109    125.831740523771
457.092497175424    331.253094567131
349.374485133996    357.721065463285
8.39630366380937    4.30526177658911
50.2501294702745    31.1539961383794
51.2772385586404    66.8937884059372
169.473350033569    117.993461506227
47.5601861370703    41.0301951390256
238.568680512591    271.103448196271
122.668905036686    92.7991203760259
710.506330695352    568.473304793075
14.1193442910318    11.2664752571536
29.6858453280301    41.0915584209232
78.9811024872745    98.557906977124
143.137824860583    200.312672914717
228.952312559228    208.952150636992
414.93711559597 364.157958616779
193.573470074735    156.743939369768
151.710594739511    165.182915986475
16.3790389361525    62.1220611327726
63.6344501007354    81.4281142367824
52.6876908746722    58.4074520261634
356.890313613082    426.263965724419
4.0847500724139 4.13161532597561
233.32353554667 185.840713238473
4.71348339142599    16.7565881676473
89.4105877815801    55.7427731671095
162.930238504639    91.1574660327713
27.6720869896949    30.8456197258235
107.041950691333    17.5365838616139
132.491703246086    94.8472761626705
165.348305450273    118.806052283819
428.453296492502    438.259964898252
38.5832188166168    20.0643402347992

-- 
Sucheta Tripathy, Ph.D.
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

web page: http://staff.vbi.vt.edu/sutripa
blog    : http://genomics-array.blogspot.com/
quick ref:
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html