Question Of Error Using Pamr

Question

[proxify]

I am trying to get some data processed with PAMR however I constantly get this error:

object of type 'closure' is not subsettable

The command I'm trying to execute is:

data$x<- read.table("GSE8607_series_matrix_pamr.txt", sep="\t")

Here's an extract of my data:

ID_REF:Affymetrix    GSM213467    GSM213468    GSM213469    GSM213470    GSM213471    GSM213472    GSM213473    GSM213474    GSM213475    GSM213476    GSM213477    GSM213478    GSM213479    GSM213480    GSM213481    GSM213482    GSM213483    GSM213484    GSM213485    GSM213486    GSM213487    GSM213488    GSM213489    GSM213490    GSM213491    GSM213492    GSM213493    GSM213494    GSM213495    GSM213496    GSM213497    GSM213498    GSM213499    GSM213501    GSM213502    GSM213503    GSM213504    GSM213505    GSM213506    GSM213507    GSM213508    GSM213509    GSM213510
#class    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa1    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4    Etapa4 "1000_at"    1413.83    1514.82    1348.94    2172.53    892.271    1294.55    809.316    1241.71    1136.22    734.243    948.142    1075.58    1090.9    1064.72    898.675    1141.47    925.75    1163.61    1044.09    1075.53    2117.86    1987.66    902.812    1745.59    1630.86    1944.59    862.752    1446.76    910.196    1001.82    917.932    960.058    1220.9    1420.46    1396.41    939.36    1184.71    861.708    1137.66    1684.18    1517.35    2148.55    1573.16 "1001_at"    92.1566    65.2595    103.024    460.925    121.657    186.35    133.224    89.2561    29.9992    75.741    128.287    138.454    112.218    204.446    138.836    142.738    121.785    148.701    122.207    92.7091    70.9685    291.417    140.37    181.268    266.055    347.586    125.264    302.187    122.348    89.5844    161.026    102.472    182.084    111.624    141.402    119.162    146.068    61.556    123.777    366.309    114.768    66.5499    86.8179 "1002_f_at"    21.8172    43.2422    20.7109    186.968    17.8681    35.8325    70.9926    27.7219    89.4961    49.624    49.3047    55.329    52.3349    27.0831    17.8611    32.2348    49.3057    66.6912    30.6116    22.7418    147.276    335.494    39.7379    7.25751    46.7628    97.5076    26.5286    22.3532    53.4994    35.264    92.2511    29.9185    231.239    20.1712    12.3882    22.5304    103.632    41.2218    75.5324    138.411    65.7054    75.2798    39.6764 "1003_s_at"    26.9999    26.6193    41.5755    50.484    330.733    246.752    200.234    42.9983    81.4183    217.867    51.496    214.387    107.879    63.6559    85.4732    84.1175    100.312    228.603    124.966    109.989    68.3454    248.319    195.605    386.688    80.453    201.535    43.701    106.941    63.7569    57.758    163.532    42.5553    162.722    74.0284    98.0253    165.305    81.8241    142.843    116.116    44.3205    284.094    79.47    81.5479 "1004_at"    35.9134    73.1345    21.8214    684.947    702.481    90.4352    328.316    89.9075    112.308    253.557    184.909    299.436    402.331    204.794    234.799    172.397    151.173    383.339    313.459    277.196    348.811    283.15    280.292    1248.75    243.092    238.15    123.545    256.75    157.425    241.232    325.219    278.9    82.2522    240.092    188.441    367.044    304.057    235.924    293.364    62.8265    223.886    464.647    172.791 "1005_at"    548.452    568.115    1947.51    475.402    716.041    566.791    830.457    713.838    407.64    1215.28    1207.97    522.877    1136.99    5351.64    446.935    838.358    584.457    410.117    356.605    415.075    509.889    144.122    472.874    185.007    512.708    64.9194    590.681    309.45    630.001    968.632    742.527    1090.19    122.305    225.481    317.38    1288.17    2183.55    462.014    257.57    778.23    81.5677    649.825    295.857 "1006_at"    50.0263    6.02078    80.4661    58.5581    6.45041    15.8062    6.01295    6.81831    9.47086    9.50754    7.00971    2.93539    24.8264    6.60019    7.56652    4.46223    7.49979    11.1001    6.91017    5.44199    21.4446    20.5042    6.39556    20.4825    102.489    41.6693    11.2836    11.2706    10.9046    3.74402    12.5883    15.2708    59.8245    22.7277    13.0799    21.8956    20.736    9.87517    11.0357    9.20369    92.4146    340.239    11.2847 "1007_s_at"    1212.07    1171.33    1077.27    4743.55    1907.68    2535.7    1785.48    3178.63    2212.49    2611.96    2620.62    1953    1914.37    1678.63    3657.57    2695.61    3015    1384.46    1908.98    2047.69    3009.99    2747.86    1347.85    1630.23    3206.11    3542.94    2014.71    2220.45    2700.56    3828.45    3694.32    3045.96    3954.91    3498.62    2233.02    2741.7    1795.1    2458.32    2633.81    2833.07    5805.37    3738.96    2559.2 "1008_f_at"    675.792    1408.48    1035.56    939.012    845.605    1815.19    1395.61    1771.85    850.641    1358.36    1501.38    1504.62    466.012    1237.49    2953.05    1231.16    1104.03    1080.73    1352.31    813.176    1063.31    3185.62    2176.2    1609.42    1619.71    1278.68    631.816    762.823    5095.18    2447.39    3126.11    1147.77    524.923    731.171    551.561    2465.4    2985.2    805.253    1494.81    1576.09    2804.06    1515.52    3502.3

I can't seem to find the problem, could anybody help please?

Answer 1

[Neilfws]

You are using read.table incorrectly. The variable data$x refers to one column in the data frame named data, with the name x. Clearly, you cannot read a multi-column file into one column of a data frame.

Try this instead:

data<- read.table("GSE8607_series_matrix_pamr.txt", sep="\t")

You may also need to add header=T as an argument to read.table() if GSE8607_series_matrix_pamr.txt has a header row.

[proxify]

this fixed it, thanks! I am trying to follow the tutorial but overall I'm new to this field so still getting the hang of it =)

[Neilfws]

Now that I think about it, data$x could refer to a list (data) where element x is a data frame. However, that is not clear on the tutorial page that you mentioned on Twitter.