Hello all,
I am trying to use geNorm in R to get some housekeeping genes selected. But I can't seem to get read.qPCR to play nice. I am getting the error: "Error in levels(raw.data$Sample) <- make.names(levels(raw.data$Sample)) :
attempt to set an attribute on NULL"
I've tried to debug it but haven't made any progress.
Using the code:
## Load packages and read in data
rm(list = ls())
library(ReadqPCR)
library(NormqPCR)
library(RColorBrewer)
setwd("...")
data <- read.qPCR(file.path(getwd(), "HK_test_2.csv"), verbose = TRUE)
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] NormqPCR_1.18.0 qpcR_1.4-0 Matrix_1.2-6 robustbase_0.92-6
[5] rgl_0.95.1441 minpack.lm_1.2-0 MASS_7.3-45 RColorBrewer_1.1-2
[9] ReadqPCR_1.18.0 affy_1.50.0 Biobase_2.32.0 BiocGenerics_0.18.0
loaded via a namespace (and not attached):
[1] lattice_0.20-33 grid_3.3.1 BiocInstaller_1.22.3
[4] zlibbioc_1.18.0 affyio_1.42.0 preprocessCore_1.34.0
[7] tools_3.3.1 DEoptimR_1.0-6
Here is my data:
Well | Plate | Sample | Detector | Cq |
1 | A | 021A | 18S | 8.803287 |
2 | A | 021A | 18S | 8.508816 |
3 | A | 021A | 18S | 8.585903 |
217 | A | RL | 18S | 11.900922 |
218 | A | RL | 18S | 12.948908 |
219 | A | RL | 18S | 12.144265 |
241 | A | TM | 18S | 17.846718 |
242 | A | TM | 18S | 18.769756 |
243 | A | TM | 18S | 17.362099 |
265 | A | PJ | 18S | 10.598029 |
266 | A | PJ | 18S | 10.433856 |
267 | A | PJ | 18S | 10.064806 |
25 | A | 063A | 18S | 12.242322 |
26 | A | 063A | 18S | 12.593292 |
27 | A | 063A | 18S | 12.114765 |
49 | A | 060A | 18S | 9.493462 |
50 | A | 060A | 18S | 10.679368 |
51 | A | 060A | 18S | 10.765488 |
73 | A | 041B | 18S | 14.339015 |
74 | A | 041B | 18S | 14.259873 |
75 | A | 041B | 18S | 14.085783 |
97 | A | 051B | 18S | 12.157936 |
98 | A | 051B | 18S | 12.2892475 |
99 | A | 051B | 18S | 12.8351345 |
121 | A | 033B | 18S | 6.412091 |
123 | A | 033B | 18S | 6.3336864 |
145 | A | 033B | 18S | 6.2269382 |
146 | A | 014C | 18S | 6.3709683 |
147 | A | 014C | 18S | 6.049335 |
169 | A | 014C | 18S | 4.625241 |
170 | A | 012C | 18S | 6.4697356 |
171 | A | 012C | 18S | 5.83666 |
193 | A | 029C | 18S | 6.9204807 |
194 | A | 029C | 18S | 6.2429805 |
195 | A | 029C | 18S | 6.620584 |
4 | A | 021A | ACTB | 18.680311 |
5 | A | 021A | ACTB | 18.562038 |
6 | A | 021A | ACTB | 18.564909 |
220 | A | RL | ACTB | 21.911484 |
221 | A | RL | ACTB | 22.088778 |
244 | A | RL | ACTB | 24.082993 |
245 | A | TM | ACTB | 23.97992 |
246 | A | TM | ACTB | 24.439238 |
268 | A | PJ | ACTB | 20.58492 |
269 | A | PJ | ACTB | 20.603588 |
28 | A | 063A | ACTB | 22.284512 |
29 | A | 063A | ACTB | 22.306473 |
30 | A | 063A | ACTB | 22.322071 |
52 | A | 060A | ACTB | 19.82482 |
53 | A | 060A | ACTB | 19.802439 |
54 | A | 060A | ACTB | 19.87252 |
76 | A | 041B | ACTB | 24.894167 |
77 | A | 041B | ACTB | 24.873465 |
78 | A | 041B | ACTB | 25.026762 |
100 | A | 051B | ACTB | 22.299055 |
101 | A | 051B | ACTB | 22.667458 |
102 | A | 051B | ACTB | 22.543547 |
124 | A | 033B | ACTB | 20.593384 |
125 | A | 033B | ACTB | 20.64025 |
126 | A | 033B | ACTB | 20.726015 |
148 | A | 014C | ACTB | 19.760023 |
149 | A | 014C | ACTB | 19.84839 |
150 | A | 014C | ACTB | 19.978727 |
172 | A | 012C | ACTB | 19.871353 |
173 | A | 012C | ACTB | 20.002136 |
174 | A | 012C | ACTB | 20.155916 |
196 | A | 029C | ACTB | 22.216824 |
197 | A | 029C | ACTB | 22.174309 |
11 | A | 021A | ATP5B | 24.432343 |
12 | A | 021A | ATP5B | 24.236248 |
226 | A | RL | ATP5B | Undetermined |
227 | A | RL | ATP5B | 24.960196 |
228 | A | RL | ATP5B | 25.434181 |
250 | A | TM | ATP5B | 33.543446 |
251 | A | TM | ATP5B | 25.457857 |
252 | A | TM | ATP5B | 24.519125 |
274 | A | PJ | ATP5B | Undetermined |
275 | A | PJ | ATP5B | 24.988977 |
276 | A | PJ | ATP5B | 24.579456 |
34 | A | 063A | ATP5B | Undetermined |
35 | A | 063A | ATP5B | 25.695545 |
36 | A | 063A | ATP5B | 25.80395 |
58 | A | 060A | ATP5B | Undetermined |
59 | A | 060A | ATP5B | 23.875486 |
60 | A | 060A | ATP5B | 24.711098 |
82 | A | 041B | ATP5B | Undetermined |
83 | A | 041B | ATP5B | 28.596996 |
84 | A | 041B | ATP5B | 27.998041 |
106 | A | 051B | ATP5B | Undetermined |
107 | A | 051B | ATP5B | 26.341555 |
108 | A | 051B | ATP5B | 26.933447 |
130 | A | 033B | ATP5B | Undetermined |
131 | A | 033B | ATP5B | 25.844624 |
132 | A | 033B | ATP5B | 25.72582 |
154 | A | 014C | ATP5B | Undetermined |
155 | A | 014C | ATP5B | 24.584467 |
156 | A | 014C | ATP5B | 25.147861 |
178 | A | 012C | ATP5B | Undetermined |
179 | A | 012C | ATP5B | 24.269608 |
180 | A | 012C | ATP5B | 24.364819 |
202 | A | 029C | ATP5B | Undetermined |
203 | A | 029C | ATP5B | 25.740673 |
204 | A | 029C | ATP5B | 26.006191 |
I would really appreciate any advice as to how to remedy this?
Thanks,
Tim