Replicating read.qPCR - "attribute on NULL"
0
0
Entering edit mode
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
ADD COMMENT

Login before adding your answer.

Traffic: 639 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6