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]

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