[BioC] problems normalizing in limma
Anand C.Patel
acpatel at usa.net
Thu Oct 13 02:35:32 CEST 2005
I'm having troubles with some new arrays we're working with.
After some effort, I've managed to read .csv output from PerkinElmer ScanArray
into an RGList object.
Warning to anyone else -- the .gpr files this program generates do not conform
strictly to the gpr file format, and will make both limma and marray very
unhappy.
I have a gal file which appears to correctly identify block, column, row, ID,
and name, and have even managed to make a SpotTypes file that shows me the
control probes.
The RGList looks like this (sorry for the large message):
> RG2
An object of class "RGList"
$R
slide_13295067 slide_13295072 slide_13295071 slide_13295073
slide_13295075 slide_13295079 slide_13295080 slide_13295203 slide_13295068
slide_13295214
[1,] 61323 57928 57404 55737
61890 58153 63823 53921 57871
59289
[2,] 57955 51322 55691 60830
48322 64418 59731 47373 53971
54898
[3,] 1057 3361 1050 1097
1651 1174 1349 2176 1220
1471
[4,] 3185 7716 5754 5925
5850 8287 8498 6246 3255
7011
[5,] 1306 810 1069 533
978 1485 277 326 1190
679
slide_13295879 slide_13295887
[1,] 58546 58522
[2,] 59005 61561
[3,] 1440 1566
[4,] 13061 12547
[5,] 24787 648
38972 more rows ...
$G
slide_13295067 slide_13295072 slide_13295071 slide_13295073
slide_13295075 slide_13295079 slide_13295080 slide_13295203 slide_13295068
slide_13295214
[1,] 59066 58672 47495 47399
63671 59502 53084 62982 55238
52893
[2,] 52584 54957 39850 50818
54542 62064 47929 57410 48840
49985
[3,] 2443 1444 812 2001
598 1127 2465 1558 1308
1148
[4,] 5249 6511 2926 7372
4312 5657 10363 8768 2464
6809
[5,] 1662 1060 481 954
936 1071 608 920 512
438
slide_13295879 slide_13295887
[1,] 57486 51338
[2,] 58792 56861
[3,] 959 1349
[4,] 12943 9490
[5,] 776 994
38972 more rows ...
$Rb
slide_13295067 slide_13295072 slide_13295071 slide_13295073
slide_13295075 slide_13295079 slide_13295080 slide_13295203 slide_13295068
slide_13295214
[1,] 172 193 186 208
220 174 205 237 183
185
[2,] 168 191 183 252
197 214 195 204 202
259
[3,] 140 151 145 150
157 146 151 185 142
215
[4,] 148 144 155 153
147 152 149 190 152
182
[5,] 133 140 147 147
132 143 147 185 144
147
slide_13295879 slide_13295887
[1,] 208 228
[2,] 210 230
[3,] 171 152
[4,] 147 143
[5,] 152 145
38972 more rows ...
$Gb
slide_13295067 slide_13295072 slide_13295071 slide_13295073
slide_13295075 slide_13295079 slide_13295080 slide_13295203 slide_13295068
slide_13295214
[1,] 252 250 261 319
301 285 355 588 301
319
[2,] 247 273 280 300
279 294 324 568 251
310
[3,] 190 197 208 246
219 187 265 497 223
249
[4,] 185 198 219 247
244 179 263 473 217
239
[5,] 177 206 210 242
278 196 248 501 233
247
slide_13295879 slide_13295887
[1,] 310 270
[2,] 287 286
[3,] 237 197
[4,] 223 222
[5,] 233 226
38972 more rows ...
$targets
[1] "slide_13295067.csv" "slide_13295072.csv" "slide_13295071.csv"
"slide_13295073.csv" "slide_13295075.csv"
7 more rows ...
$genes
Block Column Row ID Name
Status
1 1 1 1 mCP000073 gi|21070949|ref|NM_019639.2|_151
control
2 1 2 1 mCP000085 gi|21070949|ref|NM_019639.2|_151
control
3 1 3 1 mCT000169 NM_008512.90|chr10|-|127557334|127558231_72
control
4 1 4 1 mCP000181 gi|31981889|ref|NM_009735.2|_43
control
5 1 5 1 mCT000265 NM_011701.9|chr2|+|13576298|13576633_142
control
38971 more rows ...
$printer
$ngrid.r
[1] 12
$ngrid.c
[1] 4
$nspot.r
[1] 28
$nspot.c
[1] 29
attr(,"class")
[1] "PrintLayout"
Trying to normalize with either loess or robustspline yields:
> MA <- normalizeWithinArrays(RG2)
Error in switch(method, loess = { : printer layout information does not match
M row dimension
> MA <- normalizeWithinArrays(RG2, method="robustspline")
Loading required package: MASS
Loading required package: splines
Error in normalizeRobustSpline(object$M[, j], object$A[, j], layout, df = df,
:
(subscript) logical subscript too long
Both suggest that something is amiss with my layout information, but I cannot
begin to imagine how to diagnose the exact problem.
Help!
Thanks,
Anand C. Patel, MD
Washington University School of Medicine
acpatel at usa.net
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