On May 31, 2009, at 10:49 AM, Hongyuan Cao wrote:
x = read.table("hongyuan_5_30_forsafe.txt", sep = "\t")
> x = read.table("/Users/davidwinsemius/Downloads/
hongyuan_5_30_forsafe.txt", sep = "\t")
> str(x)
'data.frame': 7131 obs. of 74 variables:
$ V1 : Factor w/ 7131 levels "","A28102_at",..: 1 934 120 122 118
126 124 130 128 134 ...
$ V2 : Factor w/ 5528 levels "","2-Sep","6-Mar",..: 1 5528 NA NA NA
NA NA NA NA NA ...
$ V3 : Factor w/ 2375 levels "-1","-10","-100",..: 2374 2375 195 106
499 2262 287 483 1254 143 ...
$ V4 : Factor w/ 2326 levels "-1","-10","-100",..: 2325 2326 75 533
1 1442 231 357 299 117 ...
My guess (which became a conclusion after testing) was that you have
encountered the stringsAsFactors pitfall. (It's probably in the R
Inferno someplace bu my favorite quote is from Terry Terneau:
.)
Try reading the table in with stringsAsFactors=FALSE or as.is=TRUE.
After doing that and applying the rest of your code, I get:
> head(y)
X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
X11 X12 X13 X14 X15 X16 X17
AFFX-BioB-5_at -214 -139 -76 -135 -106 -138 -72 -413 5 -88
-165 -67 -92 -113 -107 -117 -476
AFFX-BioB-M_at -153 -73 -49 -114 -125 -85 -144 -260 -127 -105
-155 -93 -119 -147 -72 -219 -213
AFFX-BioB-3_at -58 -1 -307 265 -76 215 238 7 106 42
-71 84 -31 -118 -126 -50 -18
AFFX-BioC-5_at 88 283 309 12 168 71 55 -2 268 219
82 25 173 243 149 257 301
AFFX-BioC-3_at -295 -264 -376 -419 -230 -272 -399 -541 -210 -178 -163
-179 -233 -127 -205 -218 -403
AFFX-BioDn-5_at -558 -400 -650 -585 -284 -558 -551 -790 -535 -246 -430
-323 -227 -398 -284 -402 -394
.....
...snipped the rest of the output.
You replied to me only personally which is against R-help practice, so
I am adding back the list to the address list.
(You should also configure your maile-client so that it sends plain
text to the r-help list.)
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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