[BioC] replace error reading 2color txt data into limma

[Susan J. Miller]

I am hoping someone can tell me what is causing this problem.  I am 
using R 2.1.0, limma 2.0.2 on a Windows 2000 system. I have four .txt 
files containing 2-color microarray data.  If I read each individual txt 
file it seems to work, but when I try to read all of the files I get the 
error shown below:

 > RG=read.maimages("C1_vs_O1.txt",columns=list(Rf="Spot Median 
Intensity (w685)",Gf="Spot Median Intensity (w595)",Rb="Background 
Median Intensity (w685)",Gb="Background Median Intensity (w595)"))
Read C1_vs_O1.txt

(seems OK)

 > RG=read.maimages(ext="txt",columns=list(Rf="Spot Median Intensity 
(w685)",Gf="Spot Median Intensity (w595)",Rb="Background Median 
Intensity (w685)",Gb="Background Median Intensity (w595)"))
Read C1_vs_O1.txt
Error in "[<-"(`*tmp*`, , i, value = c(168, 175, 265, 313, 32495, 32475, 
  : number of items to replace is not a multiple of replacement length

The first four lines in the file C1_vs_O1.txt are:
Number	Name	Array/Plate	Flagged As	Control Spot	Multi-Set	Multi-Set Row 
Multi-Set Column	Set	Set Row	Set Column	Row	Column	Comments	Clone ID 
UniGene cluster ID	Gene symbol	Locus ID	Chromosome ID	GenBank 
accession number	Tissue	Gene map	Gene name	Organism	Sequence	Detection 
Method (w595)	Detection Method (w685)	Detection Status (w595)	Detection 
Status (w685)	X Centroid (pixels) (w595)	X Centroid (pixels) (w685)	Y 
Centroid (pixels) (w595)	Y Centroid (pixels) (w685)	X Spot Deviation 
(um) (w595)	X Spot Deviation (um) (w685)	Y Spot Deviation (um) (w595)	Y 
Spot Deviation (um) (w685)	X Set Deviation (um) (w595)	X Set Deviation 
(um) (w685)	Y Set Deviation (um) (w595)	Y Set Deviation (um) (w685) 
Major Extent (um) (w595)	Major Extent (um) (w685)	Minor Extent (um) 
(w595)	Minor Extent (um) (w685)	Compactness (%) (w595)	Compactness (%) 
(w685)	Threshold (w595)	Threshold (w685)	Spot Saturation (%) (w595)	Spot 
Saturation (%) (w685)	Spot Mean Intensity (w595)	Spot Mean Intensity 
(w685)	Spot Median Intensity (w595)	Spot Median Intensity (w685)	Spot 
Standard Deviation (w595)	Spot Standard Deviation (w685)	Spot Number of 
Pixels (w595)	Spot Number of Pixels (w685)	Spot Total Intensity (w595) 
Spot Total Intensity (w685)	Spot Peak Intensity (w595)	Spot Peak 
Intensity (w685)	Background Mean Intensity (w595)	Background Mean 
Intensity (w685)	Background Median Intensity (w595)	Background Median 
Intensity (w685)	Background Standard Deviation (w595)	Background 
Standard Deviation (w685)	Background Number of Pixels (w595)	Background 
Number of Pixels (w685)	Spot Confidence (w595)	Spot Confidence (w685) 
Spot Normalized Intensity (w595)	Spot Normalized Intensity (w685)	Spot 
Ratio (w595)	Spot Ratio (w685)	Spot SNR (w595)	Spot SNR (w685)	Spot CV 
(%) (w595)
1	A1_AB	IGERT_C1vsO1_11_10_04	NORMAL	NO	1	1	1	A	1	1	1	1	None	None 
None	None	None	None	None	None	None	None	None	None	AUTO	AUTO	DETECTED 
DETECTED	122.388885	122.388885	19.125	19.125	13.961801	13.961801 
-7.780155	-7.780155	-9.756	-9.756	0	0	10.134623	10.134623	9.486059 
9.486059	34.932919	34.932919	338	338	0	0	225.117279	117.413582	216 
115	40.293694	25.080153	162	162	36469	19021	317	184	174.990311 
86.96489	174	86	15.307359	12.753221	826	826	100	100	42	29	1.448276 
0.690476	3.274698	2.38753	74.356911
2	A1_AB	IGERT_C1vsO1_11_10_04	NORMAL	NO	1	1	1	A	1	1	1	2	None	None 
None	None	None	None	None	None	None	None	None	None	AUTO	AUTO	DETECTED 
DETECTED	150.583328	150.583328	19.666666	19.666666	17.027	17.027 
-2.151189	-2.151189	-9.756	-9.756	0	0	10.197981	10.197981	9.409546 
9.409546	46.076748	46.076748	377	377	0	0	252.658386	129.621124	239 
124	46.958637	25.637608	161	161	40678	20869	404	229	197.486191 
101.923172	197	103	19.706385	15.429781	833	833	100	100	42	21	2	0.5 
2.799712	1.795097	77.255592
3	A2_AB	IGERT_C1vsO1_11_10_04	NORMAL	NO	1	1	1	A	1	1	1	3	None	None 
None	None	None	None	None	None	None	None	None	None	AUTO	AUTO	DETECTED 
DETECTED	177.301987	177.301987	18.797029	18.797029	5.694523	5.694523 
-10.29089	-10.29089	-9.756	-9.756	0	0	11.567095	11.567095	9.996995 
9.996995	19.474066	19.474066	521	521	0	0	400.362488	219.306244	393 
213	108.947014	62.532211	160	160	64058	35089	685	387	228.681213 
121.866669	224	119	29.274176	18.376568	825	825	100	100	169	94 
1.797872	0.556213	5.864598	5.302382	61.125092


If anyone can tell me how to get around this problem I would be grateful 
for the help!

Thanks,

Susan J. Miller
Biotechnology Computing Facility
Arizona Research Laboratories
University of Arizona
Tucson, AZ  85721
(520) 626-2597