[BioC] read.ilmn Error in 'colnames<-'...
Wei Shi
shi at wehi.EDU.AU
Mon Apr 16 07:35:44 CEST 2012
Dear Katrina,
It seems the problem is that your control probe profile file does not have a column called "TargetID". This column gives the types of control probes such as 'negative','housekeeping' etc., and it is normally included in the control probe profile generated by Illumina GenomeStudio.
The read.ilmn function first reads in the regular probe profile ("2011-238-sample-probe-profile.txt"), and then reads in the control probe profile ("2011-238 control probe profile.txt"), and finally merges them together. Because the control probe profile have one less column, an error occurred when it was merged with the regular probe profile. You will need to have this column in the control probe profile so that the negative control probes can be extracted to be used in the subsequent normalization step.
Could you show me the first several lines of your control probe profile file? A possibility is that the 'TargetID' column may have a different name in your file which read.ilmn fails to recognize (read.ilmn looks for keywords 'TargetID' and 'Symbol').
Cheers,
Wei
On Apr 14, 2012, at 2:17 AM, Katrina Bogan wrote:
> Hi,
>
> I recently performed an experiment using the Illumina Human HT-12 v4.0 chip. I am trying to use the read.ilmn function to read in my sample probe profile and my control probe profile (as it is done in the Bead Array Use Cases vignette) and I am getting the following error message (highlighted in red):
>
> cufi <- read.ilmn(files = "2011-238-sample-probe-profile.txt", ctrlfiles = "2011-238 control probe profile.txt", other.columns = "Detection")
> Reading file 2011-238-sample-probe-profile.txt ... ...
> Reading file 2011-238 control probe profile.txt ... ...
>
> Error in `colnames<-`(`*tmp*`, value = c("PROBE_ID", "SYMBOL", "Status" :
> 'names' attribute [3] must be the same length as the vector [2]
>
> Each file can be read with read.ilmn independently (as you can see below), but not together, as (I think) it needs to be done . I've provided the code and the data it returns.
>
> Thank you in advance for any insight or help. In addition, if anyone has any information regarding whether it is normal for the detection of the control probe profile to read zero (highlighted in purple) I would very much appreciate it! My suspicion is that this is not normal, though illumine tech support will not confirm.
>
> Best,
> Katrina
>
>
> cufi <- read.ilmn(files = "2011-238-sample-probe-profile.txt", other.columns = "Detection")
> Reading file 2011-238-sample-probe-profile.txt ... ...
> cufi
> An object of class "EListRaw"
> $source
> [1] "illumina"
>
> $E
> 7018887037_A 7018887037_B 7018887037_C 7018887037_D 7018887037_E 7018887037_F 7018887037_G
> ILMN_1762337 109.8470 112.3501 111.6334 118.5278 102.55490 108.4022 121.1064
> ILMN_2055271 152.4279 150.7404 138.8105 139.7926 123.63680 130.0332 142.0012
> ILMN_1736007 101.1144 101.6223 108.8634 106.5286 92.56808 106.5077 118.2387
> ILMN_2383229 114.0005 102.2975 106.6898 110.9575 102.82950 100.5731 113.5714
> ILMN_1806310 112.6651 112.4650 127.4782 114.3911 118.89690 107.9589 120.0937
> 7018887037_H 7018887037_I 7018887037_J 7018887037_K 7018887037_L
> ILMN_1762337 117.9175 104.8866 116.1791 105.8730 110.8641
> ILMN_2055271 121.0683 139.7709 138.7806 113.2753 134.1487
> ILMN_1736007 122.1134 108.0759 106.7737 106.4517 109.4490
> ILMN_2383229 102.3755 107.1944 113.2953 103.6022 101.8368
> ILMN_1806310 118.7865 122.7471 111.6379 118.4983 103.5502
> 47226 more rows ...
>
> $genes
> PROBE_ID SYMBOL
> 1 ILMN_1762337 7A5
> 2 ILMN_2055271 A1BG
> 3 ILMN_1736007 A1BG
> 4 ILMN_2383229 A1CF
> 5 ILMN_1806310 A1CF
> 47226 more rows ...
>
> $targets
> [1] "7018887037_A" "7018887037_B" "7018887037_C" "7018887037_D" "7018887037_E"
> 7 more rows ...
>
> $other
> $Detection
> 7018887037_A 7018887037_B 7018887037_C 7018887037_D 7018887037_E 7018887037_F 7018887037_G
> ILMN_1762337 0.589610400 0.40909090 0.51168830 0.17142860 0.79610390 0.67142860 0.22467530
> ILMN_2055271 0.005194805 0.01298701 0.03376623 0.01168831 0.04675325 0.05974026 0.02077922
> ILMN_1736007 0.951948000 0.87532470 0.63376620 0.66493510 0.99870130 0.77012990 0.32857140
> ILMN_2383229 0.393506500 0.85844150 0.74675330 0.41298700 0.78181820 0.95454540 0.52337660
> ILMN_1806310 0.454545500 0.40389610 0.09610390 0.28311690 0.10259740 0.69740260 0.25714290
> 7018887037_H 7018887037_I 7018887037_J 7018887037_K 7018887037_L
> ILMN_1762337 0.3064935 0.80259740 0.39090910 0.5779221 0.254545500
> ILMN_2055271 0.1935065 0.01818182 0.02597403 0.2324675 0.007792208
> ILMN_1736007 0.1649351 0.66493510 0.84415580 0.5415584 0.323376600
> ILMN_2383229 0.9506493 0.70909090 0.52727270 0.6896104 0.712987000
> ILMN_1806310 0.2753247 0.12077920 0.60519480 0.1142857 0.628571500
> 47226 more rows ...
>
>
> cufi <- read.ilmn(ctrlfiles = "2011-238 control probe profile.txt", other.columns = "Detection")
> Reading file 2011-238 control probe profile.txt ... ...
> cufi
> An object of class "EListRaw"
> $source
> [1] "illumina"
>
> $E
> 7018887037_A 7018887037_B 7018887037_C 7018887037_D 7018887037_E 7018887037_F 7018887037_G 7018887037_H
> 5090180 22060.7400 19370.6600 17668.7700 19173.3800 21444.520 22304.1800 22956.020 20552.0300
> 6510136 14550.5000 14012.8700 14959.7500 15234.9600 14586.330 13388.7900 14746.870 13197.1600
> 1110170 25425.7400 19953.8900 24881.2200 24772.7700 23155.870 23433.1800 31479.600 22471.8700
> 1450438 372.9037 349.3491 360.1076 396.7065 391.752 354.3141 383.672 396.9438
> 2510500 4008.0100 3534.1340 3473.2170 4051.0800 3606.757 3564.2820 4414.159 4052.6210
> 7018887037_I 7018887037_J 7018887037_K 7018887037_L
> 5090180 19812.1800 23653.8400 22141.8100 24106.7100
> 6510136 14103.5400 17526.1400 15614.7800 15747.4900
> 1110170 25447.5100 26360.6000 27778.8600 27455.6600
> 1450438 369.1837 405.6142 432.7088 426.5763
> 2510500 4054.9660 3942.7390 3994.1830 4259.5820
> 882 more rows ...
>
> $genes
> ProbeID Status
> 1 5090180 5090180
> 2 6510136 6510136
> 3 1110170 1110170
> 4 1450438 1450438
> 5 2510500 2510500
> 882 more rows ...
>
> $targets
> [1] "7018887037_A" "7018887037_B" "7018887037_C" "7018887037_D" "7018887037_E"
> 7 more rows ...
>
> $other
> $Detection
> 7018887037_A 7018887037_B 7018887037_C 7018887037_D 7018887037_E 7018887037_F 7018887037_G 7018887037_H
> 5090180 0 0 0 0 0 0 0 0
> 6510136 0 0 0 0 0 0 0 0
> 1110170 0 0 0 0 0 0 0 0
> 1450438 0 0 0 0 0 0 0 0
> 2510500 0 0 0 0 0 0 0 0
> 7018887037_I 7018887037_J 7018887037_K 7018887037_L
> 5090180 0 0 0 0
> 6510136 0 0 0 0
> 1110170 0 0 0 0
> 1450438 0 0 0 0
> 2510500 0 0 0 0
> 882 more rows ...
>
>
> cufi <- read.ilmn(files = "2011-238-sample-probe-profile.txt", ctrlfiles = "2011-238 control probe profile.txt", other.columns = "Detection")
> Reading file 2011-238-sample-probe-profile.txt ... ...
> Reading file 2011-238 control probe profile.txt ... ...
> Error in `colnames<-`(`*tmp*`, value = c("PROBE_ID", "SYMBOL", "Status" :
> 'names' attribute [3] must be the same length as the vector [2]
>
> [[alternative HTML version deleted]]
>
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