Wednesday, February 20, 2013

Extract probe intensites from Affymetrix microarray using Affy Bioconductor package


If you have analysed Affimetrix microarray data using affy package, probe level intensities will be placed in a matrix e:

> e[1:30,]
             GSM470497_3%_Young_1.CEL.gz GSM470498_3%_Young_2.CEL.gz
1007_s_at                       6.300922                    6.456905
1053_at                         6.091139                    6.436253
117_at                          4.147458                    4.394540
121_at                          4.917840                    4.781082
1255_g_at                       3.911876                    3.577860
1294_at                         4.667196                    5.231878
1316_at                         3.761608                    3.994355
1320_at                         4.357223                    4.517361
1405_i_at                       3.101268                    3.180212
1431_at                         3.793192                    3.697183
1438_at                         3.832933                    3.824773
1487_at                         5.930078                    6.281960
1494_f_at                       3.702302                    3.783443
1552256_a_at                    3.681152                    4.849077
1552257_a_at                    7.317055                    7.010300
1552258_at                      5.704939                    5.237996
1552261_at                      4.573312                    5.016926
1552263_at                      4.896567                    4.895189
1552264_a_at                    4.396870                    4.417306
1552266_at                      3.765615                    3.800691
1552269_at                      3.234099                    3.315789
1552271_at                      3.332194                    3.416086
1552272_a_at                    3.375331                    3.454781
1552274_at                      3.555826                    3.733145
1552275_s_at                    5.217531                    5.242327
1552276_a_at                    3.428207                    3.699732
1552277_a_at                    7.975502                    7.625647
1552278_a_at                    3.464030                    3.693175
1552279_a_at                    4.065794                    4.587876
1552280_at                      3.105874                    3.022401
             GSM470499_3%_Young_3.CEL.gz GSM470500_3%_Old_1.CEL.gz
1007_s_at                       6.112486                  6.240159
1053_at                         6.542659                  6.440471
117_at                          4.716634                  4.495265
121_at                          4.947286                  4.812312
1255_g_at                       3.869261                  3.704167
1294_at                         5.482891                  5.673922
1316_at                         4.178375                  4.297578
1320_at                         4.611408                  4.869334
1405_i_at                       3.180604                  3.295074
1431_at                         3.663679                  3.648191
1438_at                         3.752537                  4.470490
1487_at                         6.071635                  6.587709
1494_f_at                       3.899534                  3.984177
1552256_a_at                    4.896681                  5.180593
1552257_a_at                    7.223617                  7.061115
1552258_at                      5.206598                  5.125163
1552261_at                      4.990717                  4.615066
1552263_at                      4.496287                  4.427185
1552264_a_at                    4.544224                  5.201032
1552266_at                      3.626879                  3.800691
1552269_at                      3.463972                  3.268817
1552271_at                      3.520698                  4.271798
1552272_a_at                    3.422166                  3.832704
1552274_at                      3.419513                  4.029615
1552275_s_at                    5.492400                  5.866826
1552276_a_at                    3.910554                  4.016219
1552277_a_at                    7.790630                  7.784857
1552278_a_at                    3.624583                  3.725588
1552279_a_at                    4.199384                  4.387748
1552280_at                      3.142693                  3.199028
             GSM470501_3%_Old_2.CEL.gz GSM470502_3%_Old_3.CEL.gz
1007_s_at                     6.324700                  6.456813
1053_at                       5.970385                  5.805203
117_at                        4.721467                  4.407666
121_at                        4.693134                  4.870159
1255_g_at                     3.658456                  3.457559
1294_at                       5.589966                  5.028002
1316_at                       4.346206                  4.142764
1320_at                       4.879376                  4.404180
1405_i_at                     3.141909                  3.053240
1431_at                       3.771462                  3.691278
1438_at                       3.806184                  4.127716
1487_at                       6.462532                  6.257656
1494_f_at                     4.214841                  3.808300
1552256_a_at                  4.874258                  4.795587
1552257_a_at                  6.598601                  6.351708
1552258_at                    5.001666                  5.099130
1552261_at                    5.168137                  4.943154
1552263_at                    4.176558                  4.557237
1552264_a_at                  4.733400                  4.349135
1552266_at                    3.933936                  3.349679
1552269_at                    3.413392                  3.387749
1552271_at                    4.522476                  3.445349
1552272_a_at                  4.085306                  3.552138
1552274_at                    4.213944                  3.779718
1552275_s_at                  5.609028                  5.251530
1552276_a_at                  3.941537                  3.614002
1552277_a_at                  7.665335                  7.382998
1552278_a_at                  4.121506                  3.718387
1552279_a_at                  4.701417                  4.657040
1552280_at                    2.986616                  3.028359

To extract a probe intensities for a given probe, simply type:
> e["211506_s_at",]
GSM470497_3%_Young_1.CEL.gz GSM470498_3%_Young_2.CEL.gz
                   4.445203                    4.930819
GSM470499_3%_Young_3.CEL.gz   GSM470500_3%_Old_1.CEL.gz
                   5.081375                    6.123156
  GSM470501_3%_Old_2.CEL.gz   GSM470502_3%_Old_3.CEL.gz
                   6.206172                    5.785836

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