Replicating read.qPCR - "attribute on NULL"
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t.f.jones • 0
@tfjones-11447
Last seen 6.8 years ago

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 

qpcr R • 1.2k views
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