Hi Pan,

I'm thinking the data is in the wrong format, but am keen to know if 
there's a way around this (eg remapping column headers)

 > sessionInfo()
R version 2.10.1 Patched (2009-12-29 r50852)
x86_64-apple-darwin9.8.0

locale:
[1] C/C/en_US/C/C/C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
  [1] lumi_1.12.2          MASS_7.3-4           RSQLite_0.8-1
  [4] DBI_0.2-5            preprocessCore_1.8.0 mgcv_1.6-1
  [7] affy_1.24.2          annotate_1.24.1      AnnotationDbi_1.8.1
[10] Biobase_2.6.1        ggplot2_0.8.5        digest_0.4.2
[13] reshape_0.8.3        plyr_0.1.9           proto_0.3-8
[16] JGR_1.7-0            iplots_1.1-3         JavaGD_0.5-2
[19] rJava_0.8-1

loaded via a namespace (and not attached):
[1] Matrix_0.999375-33 affyio_1.14.0      lattice_0.17-26    nlme_3.1-96
[5] tools_2.10.1       xtable_1.5-6
 >

This is the data format that I have (I've just included the first 
subject columns (in yellow))

Index 	TargetID 	ProbeID_A 	ProbeID_B 	4408100018_A.AVG_Beta 
4408100018_A.Intensity 	4408100018_A.Avg_NBEADS_A 
4408100018_A.Avg_NBEADS_B 	4408100018_A.BEAD_STDERR_A 
4408100018_A.BEAD_STDERR_B 	4408100018_A.Signal_A 
4408100018_A.Signal_B 	4408100018_A.Detection Pval 	SYMBOL 	ILMNID 
NAME 	ILMNSTRAND 	ADDRESSA_ID 	ALLELEA_PROBESEQ 	ADDRESSB_ID 
ALLELEB_PROBESEQ 	GENOMEBUILD 	CHR 	MAPINFO 	PLOIDY 	SPECIES 	SOURCE 
SOURCEVERSION 	SOURCESTRAND 	SOURCESEQ 	TOPGENOMICSEQ 	NEXT_BASE 
COLOR_CHANNEL 	TSS_COORDINATE 	GENE_STRAND 	GENE_ID 	SYNONYM 
ACCESSION 	GID 	ANNOTATION 	PRODUCT 	DISTANCE_TO_TSS 	CPG_ISLAND 
CPG_ISLAND_LOCATIONS
1 	cg00000292 	990370 	6660678 	0.7628557 	1903 	17 	26 	33.71245 
83.91733 	375 	1528 	1.83E-24 	ATP2A1 	cg00000292 	cg00000292 	TOP 
990370 	AAACATTAATTACCAACCACTCTTCCAAAAAACACTTACCATTAAAACCA 	6660678 
AAACATTAATTACCAACCGCTCTTCCAAAAAACACTTACCATTAAAACCG 	36 	16 	28797601 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGGCCTCAATGGTAAGTGTCCCTTGGAAGAGCGGCTGGTAATTAATGCCC 
TGGGGTGAGTGAGACCACGGGCCTCACCCCGGACCAAGTTAAGCGGAATCTGGAGAAATA[CG]GCCTCAATGGTAAGTGTCCCTTGGAAGAGCGGCTGGTAATTAATGCCCTCCTGCACCCCC 
	T 	Red 	28797310 	+ 	GeneID:487 	ATP2A; SERCA1; 	NM_173201.2 
GI:47132613 	isoform a is encoded by transcript variant a; 
sarcoplasmic/endoplasmic reticulum calcium ATPase 1; calcium pump 1; SR 
Ca(2+)-ATPase 1; calcium-transporting ATPase sarcoplasmic reticulum 
type; fast twitch skeletal muscle isoform; endoplasmic reticulum class 
1/2 Ca(2+) ATPase; go_component: membrane; go_component: integral to 
membrane; go_component: sarcoplasmic reticulum; go_component: smooth 
endoplasmic reticulum; go_function: ATP binding; go_function: hydrolase 
activity; go_function: nucleotide binding; go_function: calcium ion 
binding; go_function: magnesium ion binding; go_function: 
calcium-transporting ATPase activity; go_function: hydrolase activity; 
acting on acid anhydrides; catalyzing transmembrane movement of 
substances; go_process: metabolism; go_process: cation transport; 
go_process: proton transport; go_process: calcium ion transport; 
go_process: regulation of striated muscle contraction 	ATPase; Ca++ 
transporting; fast twitch 1 isoform a 	291 	TRUE 	16:28797486-28797825
2 	cg00002426 	6580397 	6100343 	0.7422037 	1343 	17 	28 	14.06707 
82.46211 	272 	1071 	2.98E-09 	SLMAP 	cg00002426 	cg00002426 	TOP 
6580397 	AATATAATAACATTACCTTACCCATCTTATAATCAAACCAAACAAAAACA 	6100343 
AATATAATAACATTACCTTACCCGTCTTATAATCAAACCAAACGAAAACG 	36 	3 	57718583 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGCTCTCGTCTGGTTTGATCACAAGACGGGCAAGGTAATGTCACCACATT 
CCGCTGTCGACCAGCGCAGAATAATGCCACTTTTGATTGCAAAGTGCTATCAAGGAACCA[CG]CTCTCGTCTGGTTTGATCACAAGACGGGCAAGGTAATGTCACCACATTGTCCAGCGGCAT 
	T 	Red 	57718214 	+ 	GeneID:7871 	SLAP; KIAA1601; 	NM_007159.2 
GI:56550042 	Sarcolemmal-associated protein; go_component: integral to 
plasma membrane; go_component: smooth endoplasmic reticulum; 
go_function: unfolded protein binding; go_process: protein folding; 
go_process: muscle contraction 	sarcolemma associated protein 	369 
TRUE 	3:57716811-57718675
3 	cg00003994 	7150184 	7150392 	0.06791084 	1829 	17 	9 	124.9058 
8.246211 	1698 	131 	5.38E-22 	MEOX2 	cg00003994 	cg00003994 	TOP 
7150184 	AATAATAATAATACCCCCTATAATACTAACTAACAAACATACCCTCTTCA 	7150392 
AATAATAATAATACCCCCTATAATACTAACTAACAAACATACCCTCTTCG 	36 	7 	15692387 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
GGTGGTGGTGGTGCCCCCTGTGATGCTGGCTGGCAAACATGCCCTCTTCG 
GGTGGTGGTGGTGGTGGTGGTGGTGCCCCCTGTGATGCTGGCTGGCAAACATGCCCTCTT[CG]TTGGGGTATCCCGCGATTATGCAAGATGAGGAAGAAGTAGAGAGCTCGGGGTAAGACATA 
	T 	Red 	15692819 	- 	GeneID:4223 	GAX; MOX2; 	NM_005924.3 
GI:55956906 	growth arrest-specific homeo box; go_component: nucleus; 
go_function: transcription factor activity; go_process: circulation; 
go_process: development; go_process: regulation of transcription; 
DNA-dependent 	mesenchyme homeo box 2 	432 	TRUE 	7:15691512-15693551
4 	cg00005847 	4850717 	1260113 	0.1226525 	7621 	15 	15 	726.3135 
101.7304 	6674 	947 	3.68E-38 	HOXD3 	cg00005847 	cg00005847 	BOT 
4850717 	TACTATAATACACCCTATATTTAAAACACTAAACTTACCCCATTAAAACA 	1260113 
TACTATAATACACCCTATATTTAAAACACTAAACTTACCCCATTAAAACG 	36 	2 	176737319 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
TACTGTAATGCACCCTGTATTTAAGGCACTGGGCTTGCCCCATTAAAGCG 
CAGATAACTCAATACTGTAATGCACCCTGTATTTAAGGCACTGGGCTTGCCCCATTAAAG[CG]CCATAAATTTGAAGGCCAATGATCGGTTTTCATGTAACGGGTGGTACTTCATACTGAAGT 
	C 	Grn 	176737051 	+ 	GeneID:3232 	HOX4; HOX1D; HOX4A; Hox-4.1; 
MGC10470; 	NM_006898.4 	GI:23510372 	homeobox protein Hox-D3; Hox-4.1; 
mouse; homolog of; homeo box D3; go_component: nucleus; go_function: 
transcription factor activity; go_process: morphogenesis; go_process: 
regulation of transcription; DNA-dependent 	homeobox D3 	268 	FALSE 	
5 	cg00006414 	6980731 	4280093 	0.07699007 	5641 	26 	19 	321.6305 
23.73005 	5199 	442 	3.68E-38 	ZNF398 	cg00006414 	cg00006414 	BOT 
6980731 	CTCAAAAACCAAACAAAACAAAACCCCAATACTAATCATTAATAAAATCA 	4280093 
CTCGAAAACCGAACAAAACAAAACCCCAATACTAATCGTTAATAAAATCG 	36 	7 	148453770 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
CTCGGAAACCGAGCAGGGCAAAACCCCAGTGCTGATCGTTAGTGGGATCG 
GAACCGGCCCAGCTCGGAAACCGAGCAGGGCAAAACCCCAGTGCTGATCGTTAGTGGGAT[CG]CGCCTGTGAATAGCCACTGCCCTCCAGCCTGGGCAACAGCCAGACCCCGTCTGTTTAATA 
	C 	Grn 	148454441 	+ 	GeneID:57541 	P51; P71; ZER6; KIAA1339; 
NM_020781.2 	GI:25777702 	isoform b is encoded by transcript variant 2; 
zinc finger DNA binding protein ZER6; zinc finger-estrogen receptor 
interaction; clone 6; zinc finger DNA binding protein p52/p71; 
go_component: nucleus; go_function: DNA binding; go_function: zinc ion 
binding; go_function: metal ion binding; go_function: transcriptional 
activator activity; go_process: transcription; go_process: regulation of 
transcription; DNA-dependent 	zinc finger 398 isoform b 	671 	TRUE 
7:148453584-148455804
6 	cg00007981 	5260689 	6860356 	0.04542967 	3554 	8 	23 	408.7077 
23.33452 	3388 	166 	3.68E-38 	PANX1 	cg00007981 	cg00007981 	TOP 
5260689 	CCAAATTCAAAAAACTACAACTAAAACTAACTATAAACAAAATAATCACA 	6860356 
CCAAATTCAAAAAACTACGACTAAAACTAACTATAAACAAAATAATCACG 	36 	11 	93502242 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
CCAAGTTCAAGGGGCTGCGACTGGAGCTGGCTGTGGACAAGATGGTCACG 
AGCCCACGGAGCCCAAGTTCAAGGGGCTGCGACTGGAGCTGGCTGTGGACAAGATGGTCA[CG]TGCATTGCGGTGGGGCTGCCCCTGCTGCTCATCTCGCTGGCCTTCGCGCAGGAGATCTCG 
	T 	Red 	93501742 	+ 	GeneID:24145 	MRS1; UNQ2529; MGC21309; 
NM_015368.3 	GI:39995063 	innexin; go_component: membrane; go_component: 
gap junction; go_component: integral to membrane 	pannexin 1 	500 
TRUE 	11:93501124-93502564
7 	cg00008493 	7200647 	2900438 	0.9610287 	13782 	16 	26 	37 
1053.25 	441 	13341 	3.68E-38 	COX8C 	cg00008493 	cg00008493 	TOP 
7200647 	CTATCTACCACAATAAATTAAAACCCAACCATCATAATAAACAAAAAACA 	2900438 
CTATCTACCGCGATAAATTAAAACCCAACCATCATAATAAACGAAAAACG 	36 	14 	92883530 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
CTGTCTGCCGCGGTGAGTTGAGGCCCAGCCATCATGGTGGGCGGGAAGCG 
CGCCAGCGGCCCCTGTCTGCCGCGGTGAGTTGAGGCCCAGCCATCATGGTGGGCGGGAAG[CG]CGTGGCCCTGGCGGGGCGCCCCGACGGGTGGGGAGAAGGGAGGACACGGCGTGCAGGCCT 
	C 	Grn 	92883290 	+ 	GeneID:341947 	COX8-3; MGC119774; MGC119775; 
NM_182971.1 	GI:33667031 	cytochrome c oxidase subunit VIII isoform 3; 
go_component: mitochondrion; go_component: integral to membrane; 
go_component: organelle inner membrane; go_function: oxidoreductase 
activity; go_function: cytochrome-c oxidase activity; go_process: 
electron transport 	cytochrome c oxidase subunit 8C 	240 	TRUE 
14:92883203-92883973
8 	cg00008713 	6860184 	3780392 	0.02229408 	29280 	17 	17 	909.5086 
68.88012 	28625 	655 	3.68E-38 	IMPA2 	cg00008713 	cg00008713 	TOP 
6860184 	CAAAACAATACAAAATTCTACACAAACCAAAAATAAAACCTATCTCAACA 	3780392 
CAAAACAATACGAAATTCTACACGAACCGAAAATAAAACCTATCTCAACG 	36 	18 	11970953 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
CAGAACAGTACGGAGTTCTGCACGAGCCGGGGGTGGGGCCTGTCTCAGCG 
GCGCGCTTGACCCAGAACAGTACGGAGTTCTGCACGAGCCGGGGGTGGGGCCTGTCTCAG[CG]CGCGGCGGTGGGGCGGGGCTTGGACACGGGCCCGGCTCAACTTGAGGGAGGCGGGGCTCG 
	C 	Grn 	11971455 	+ 	GeneID:3613 		NM_014214.1 	GI:7657235 	inosine 
monophosphatase 2; go_function: hydrolase activity; go_function: 
magnesium ion binding; go_function: inositol-1(or 4)-monophosphatase 
activity; go_process: signal transduction; go_process: phosphate 
metabolism 	inositol(myo)-1(or 4)-monophosphatase 2 	502 	TRUE 
18:11970322-11972436
9 	cg00009407 	4230376 	6380376 	0.04024385 	23357 	19 	21 	1150.749 
90.3898 	22413 	944 	3.68E-38 	TTC8 	cg00009407 	cg00009407 	BOT 
4230376 	TAACCAAATTCTACTTACAATTATTTTTCTTTTTCCTATTCTCAAACACA 	6380376 
TAACCGAATTCTACTTACGATTATTTTTCTTTTTCCTATTCTCAAACGCG 	36 	14 	88360674 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGCGCCTGAGAACAGGAAAAAGAAAAACAACCGCAAGCAGAACTCGGCTA 
GCGTCCGACTCTGCCCGGCAACCCGCGACGGCTGGGGCCTTGTCCGAGAGGTGCCCGCAG[CG]CGCCTGAGAACAGGAAAAAGAAAAACAACCGCAAGCAGAACTCGGCTACAGGGCTTGCCT 
	C 	Grn 	88360731 	+ 	GeneID:123016 	BBS8; 	NM_198309.2 	GI:53759117 
isoform B is encoded by transcript variant 2; Bardet-Biedl syndrome type 
8; go_function: binding; go_process: visual perception; go_process: 
sensory perception 	tetratricopeptide repeat domain 8 isoform B 	57 
TRUE 	14:88360520-88361283
10 	cg00010193 	4780008 	1580192 	0.7163327 	31934 	18 	24 	895.9043 
859.8419 	8987 	22947 	3.68E-38 	FLJ35816 	cg00010193 	cg00010193 	BOT 
4780008 	AAATCAAAACAAACCTAAACACTATTACAACCTAACCAAATATACACACA 	1580192 
AAATCAAAACGAACCTAAACACTATTACAACCTAACCAAATATACACACG 	36 	4 	1135216 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
AAGTCAGGGCGAGCCTGGGCACTGTTGCAGCCTGGCCAGGTGTGCACACG 
GATCTCAGAGTAAAGTCAGGGCGAGCCTGGGCACTGTTGCAGCCTGGCCAGGTGTGCACA[CG]CTCAGGGCAGTGCTAATACACCAGCCCCCTGCTGCCTCAGCACCCTCCAGACTTTAAGCA 
	C 	Grn 	1135160 	+ 	GeneID:401114 	NM_207489.1 	GI:46409601 
hypothetical protein LOC401114 	56 	FALSE 	
11 	cg00011459 	3120296 	7320368 	0.8619227 	2022 	28 	21 	11.33893 
86.55386 	193 	1829 	9.89E-29 	PMM2 	cg00011459 	cg00011459 	TOP 
3120296 	AAAAATAATCTACTATCTCCCTTTCAAACTACCCTTCTCCAAACTATACA 	7320368 
AAAAATAATCTACTATCTCCCTTTCAAACTACCCTTCTCCGAACTATACG 	36 	16 	8797926 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGCACAGCTCGGAGAAGGGCAGCCTGAAAGGGAGACAGTAGACCATTTCT 
CCACTGCAGCACCACAGCCCATGGAGAGGCCTTTCCCACACAGCTTTTCCCCGAAACCTA[CG]CACAGCTCGGAGAAGGGCAGCCTGAAAGGGAGACAGTAGACCATTTCTCTCATGGAACTC 
	T 	Red 	8799193 	+ 	GeneID:5373 	CDG1; CDGS; CDG1a; 	NM_000303.1 
GI:4557838 	phosphomannomutase activity is deficient in patients with 
the carbohydrate-deficient glycoprotein syndrome type I (CDG1); 
go_component: cytoplasm; go_function: isomerase activity; go_function: 
phosphomannomutase activity; go_function: phosphomannomutase activity; 
go_process: metabolism; go_process: mannose biosynthesis; go_process: 
GDP-mannose biosynthesis; go_process: protein amino acid N-linked 
glycosylation 	phosphomannomutase 2 	1267 	FALSE 	
12 	cg00012199 	6200228 	6200154 	0.02216047 	14295 	16 	14 	970.5 
16.25 	13976 	319 	3.68E-38 	RNASE4 	cg00012199 	cg00012199 	BOT 
6200228 	AAAACTAAAACAATAAAACACACACAATTCTAACTACACAACTATAAACA 	6200154 
AAAACTAAAACGATAAAACGCACACAATTCTAACTACGCAACTATAAACG 	36 	14 	20220864 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
GGGGCTGAGGCGGTGGGACGCACACAATTCTGACTGCGCAACTGTGAACG 
GTCGGAGAACTGGGGGCTGAGGCGGTGGGACGCACACAATTCTGACTGCGCAACTGTGAA[CG]CCGGAGAGGGCGGGCCTCCAGGCTTAGGCCCGGGCTCCCTGATGTCCTCACTTCCTGCGC 
	C 	Grn 	20222212 	+ 	GeneID:6038 	RNS4; MGC9306; 	NM_194430.1 
GI:37577169 	go_component: cellular component unknown; go_function: 
hydrolase activity; go_function: nucleic acid binding; go_function: 
endonuclease activity; go_function: pancreatic ribonuclease activity; 
go_process: mRNA cleavage 	ribonuclease; RNase A family; 4 precursor 
1348 	TRUE 	14:20220472-20221241
13 	cg00012386 	6840377 	1510390 	0.02178066 	7751 	22 	12 	406.5738 
10.23363 	7580 	171 	3.68E-38 	C1orf142 	cg00012386 	cg00012386 	BOT 
6840377 	AATTCAAATTATATTCCTAAACCCCACAATTTACAACTAATACAACCACA 	1510390 
AATTCGAATTATATTCCTAAACCCCACAATTTACAACTAATACAACCACG 	36 	1 	225989135 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGTGGTTGTACCAGTTGCAAACTGTGGGGTCCAGGAATACAACTCGAACC 
GTTTGGAGTGAGGACGGGGCCCAGGGAGATGGCATGGACCGTGCCTTTCATTTCAGGAGA[CG]TGGTTGTACCAGTTGCAAACTGTGGGGTCCAGGAATACAACTCGAACCCCAAAGAGCACA 
	T 	Red 	225989320 	+ 	GeneID:116841 	SVAP1; FLJ12517; IMAGE3451454; 
DKFZp686M10160; 	NM_053052.2 	GI:26024192 	synonyms: SVAP1; FLJ12517; 
IMAGE3451454; DKFZp686M10160 	hypothetical protein LOC116841 	185 
TRUE 	1:225989127-225990210
14 	cg00012792 	1340541 	990678 	0.02272532 	11517 	14 	15 	571.9391 
39.82193 	11253 	264 	3.68E-38 	TXNDC5 	cg00012792 	cg00012792 	BOT 
1340541 	AAAATAAAACTATACTAAAATCCACCAAAAACTATAACCCTAACACTCCA 	990678 
AAAATAAAACTATACTAAAATCCACCAAAAACTATAACCCTAACACTCCG 	36 	6 	8009492 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGGAGTGTCAGGGCTATAGTTCCTGGTGGATCCCAGCACAGCCTCATCTC 
GCAGCAAGAAGAGGGACTCCCTGGGGACTGCGGGCTCAGCGCACCTCATTATCAAGGGTA[CG]GAGTGTCAGGGCTATAGTTCCTGGTGGATCCCAGCACAGCCTCATCTCCCAGGCGGCGCC 
	T 	Red 	8009596 	- 	GeneID:81567 	ERP46; UNQ364; EndoPDI; MGC3178; 
NM_030810.2 	GI:42794770 	isoform 1 is encoded by transcript variant 1; 
thioredoxin related protein; endothelial protein disulphide isomerase; 
go_component: endoplasmic reticulum; go_function: isomerase activity; 
go_function: electron transporter activity; go_process: anti-apoptosis; 
go_process: electron transport 	thioredoxin domain containing 5 
isoform 1 	104 	TRUE 	6:8008961-8009913
15 	cg00013618 	1410673 	670594 	0.8626667 	16400 	15 	10 	168.8621 
385.2328 	2166 	14234 	3.68E-38 		cg00013618 	cg00013618 	BOT 	1410673 
CCCAAAACTATAATATTTAAAAATTCTCTACCCTCAAAAATCCCTAACCA 	670594 
CCCAAAACTATAATATTTAAAAATTCTCTACCCTCAAAAATCCCTAACCG 	36 	22 	20710839 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGGTCAGGGATCCCTGAGGGCAGAGAATTTCCAAACATCACAGTTTTGGG 
TCAGGCTAGAGGCCCGAGATAGTCAGGGAGGCTGTGGTCCCAGACTTTGAGCCAGAGAAG[CG]GTCAGGGATCCCTGAGGGCAGAGAATTTCCAAACATCACAGTTTTGGGAGCACCGTGAGA 
	C 	Grn 	20710659 	+ 	GeneID:3535 						180 	FALSE 	
16 	cg00014085 	1240274 	1780240 	0.03166901 	15562 	22 	30 	832.3356 
37.52333 	15066 	496 	3.68E-38 	RetSat 	cg00014085 	cg00014085 	BOT 
1240274 	ACCTTATTTAAAAACCTTCTTCCTAACCTCCTTATCAATTACCAAAAACA 	1780240 
ACCTTATTTAAAAACCTTCTTCCTAACCTCCTTATCAATTACCAAAAACG 	36 	2 	85435016 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGCCCCTGGTAACTGACAAGGAGGCCAGGAAGAAGGTTCTCAAACAAGGT 
TGGGACTATTCTCTGGCAGCTCCCCGAATCCTTTCTCCGAAGATGTCAAACGGCCCCCAG[CG]CCCCTGGTAACTGACAAGGAGGCCAGGAAGAAGGTTCTCAAACAAGGTAGCAGGAGGGAC 
	C 	Grn 	85435166 	- 	GeneID:54884 	FLJ20296; 	NM_017750.2 
GI:31377747 	go_component: nuclear outer membrane; go_component: 
endoplasmic reticulum membrane; go_function: oxidoreductase activity; 
go_function: all-trans-retinol 13;14-reductase activity; go_process: 
electron transport; go_process: retinol metabolism 
all-trans-13;14-dihydroretinol saturase 	150 	TRUE 	2:85434965-85435723
17 	cg00014837 	2970333 	2190632 	0.7356948 	1001 	21 	22 	15.92991 
38.40635 	191 	810 	0.000743657 	ACRBP 	cg00014837 	cg00014837 	TOP 
2970333 	CCTTACATAATTACCATAAAAATCCCATAAAATAAATACACTATCATTCA 	2190632 
CCTTACGTAATTACCATAAAAATCCCATAAAATAAATACACTATCATTCG 	36 	12 	6627518 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGAATGATAGTGTATCTACCTTATGGGATTCCTATGGCAATTACGTAAGG 
CCTCACGACCTGTTTGTTGGGCGAGTTGCTTCCCTAAGCCCCGATTTCTCATCTGTAAAA[CG]AATGATAGTGTATCTACCTTATGGGATTCCTATGGCAATTACGTAAGGTAGTGCATGTAA 
	T 	Red 	6626841 	- 	GeneID:84519 	SP32; OY-TES-1; 	NM_032489.2 
GI:17999523 	go_component: cellular component unknown; go_function: 
molecular function unknown; go_process: biological process unknown 
proacrosin binding protein sp32 precursor 	677 	FALSE 	
18 	cg00015770 	50767 	4730626 	0.1244575 	30087 	21 	15 	1216.783 
248.9866 	26330 	3757 	3.68E-38 	GPR103 	cg00015770 	cg00015770 	BOT 
50767 	AAACATTTTTTAATCACTAAAATCAAATCTCCCAATACTTTAACTTCCCA 	4730626 
GAACATTTTTTAATCACTAAAATCGAATCTCCCAATACTTTAACTTCCCG 	36 	4 	122521457 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	BOT 
GAACATTTTTTGGTCACTGAGATCGAGTCTCCCAGTGCTTTGGCTTCCCG 
TATTTGAACCGCGAACATTTTTTGGTCACTGAGATCGAGTCTCCCAGTGCTTTGGCTTCC[CG]CCTCTTTATCGTGGGTTTGATCCCTGAGCTGCTCTCCTTTCCCGAACCTCCCGGGGTGCA 
	C 	Grn 	122521252 	- 	GeneID:84109 	AQ27; SP9155; 	NM_198179.1 
GI:38016136 	QRFP receptor; go_component: integral to membrane; 
go_function: receptor activity; go_function: neuropeptide Y receptor 
activity; go_function: rhodopsin-like receptor activity; go_process: 
signal transduction; go_process: G-protein coupled receptor protein 
signaling pathway 	G protein-coupled receptor 103 	205 	TRUE 
4:122520698-122521834
19 	cg00016968 	5560324 	5560008 	0.8475475 	27056 	24 	19 	350.4812 
1057.567 	4040 	23016 	3.68E-38 	RHOC 	cg00016968 	cg00016968 	BOT 
5560324 	TCTAAATCCCAACTATAAATTCTATTCCCACTCCTAAATCTAACTTAACA 	5560008 
TCTAAATCCCAACTATAAATTCTATTCCCACTCCTAAATCTAACTTAACG 	36 	1 	113051971 
diploid 	Homo sapiens 	NCBI:RefSeq 	36.1 	TOP 
CGCCAAGTCAGACCTAGGAGTGGGAACAGAATTCACAGCTGGGATCCAGA 
TCCCACCTCCTCAGCTCCCTTACAGGGAAAGGAGATACGCGTGTAGGTAAATATCCTATG[CG]CCAAGTCAGACCTAGGAGTGGGAACAGAATTCACAGCTGGGATCCAGAAGCATTTCTAGG 
	C 	Grn 	113051243 	- 	GeneID:389 	ARH9; ARHC; RHOH9; 	NM_175744.3 
GI:34222243 	Aplysia RAS-related homolog 9 (oncogene RHO H9); RAS 
homolog gene family; member C (oncogene RHO H9); Aplysia ras-related 
homolog 9; go_component: membrane; go_function: GTP binding; 
go_function: nucleotide binding; go_function: GTPase activity; 
go_function: signal transducer activity; go_process: small GTPase 
mediated signal transduction; go_process: positive regulation of 
I-kappaB kinase/NF-kappaB cascade 	ras homolog gene family; member C 
728 	FALSE 	



Many thanks.

Regards,

Paul

Pan Du wrote:
> Hi Paul
>
> Please provide more detailed information, or else we cannot help you.
> For example, please send me the returns of sessionInfo() and also the top
> twenty lines of your data. I want to know whether it is because you are
> using outdated packages or data in the wrong format.
> Thanks!
>
> Pan
>
>
> On 1/16/10 5:24 PM, "gilbert feng"<g-feng@northwestern.edu>  wrote:
>
>    
>> From: Paul Sanfilippo<prseye@gmail.com>
>> Date: Sun, 17 Jan 2010 10:16:41 +1100
>> To:<bioconductor@stat.math.ethz.ch>
>> Subject: [BioC] lumiR error
>>
>> Dear List,
>>
>> I'm new to microarray analysis, so go easy.  When I try to import some
>> methylation data using lumiR, I receive the following error:
>>
>>      
>>> meth<-lumiR("~/desktop/meth_sample.txt")
>>>        
>> Error in gregexpr("\t", dataLine1) : invalid 'text' argument
>>
>> If I specify "sep":
>>
>>      
>>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
>>>        
>> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] :
>>     subscript out of bounds
>>
>> Does anyone know what might be causing the problem? Can lumiR handle
>> this type of data where headers from BeadStudio are "..._Beta" instead
>> of "..._Signal", etc
>>
>> Thank you,
>>
>> Paul Sanfilippo
>>      
>
>
> --
> Pan Du, PhD
> Research Assistant Professor
> Northwestern University Biomedical Informatics Center
> 750 N. Lake Shore Drive, 11-176
> Chicago, IL  60611
> Office (312) 503-2360; Fax: (312) 503-5388
> dupan (at) northwestern.edu
>
>
>
>
>
>    

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