Microarray analysis--exprs has probe IDs, but the column has no "ID" designation.
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5.4 years ago

Hello,

I am doing a microarray analysis. I analyze my .CEL files, normalize them with gcrma, but after I convert the data to an expression set, the probes are listed but the column has no name.

# load files
celfiles <- read.affy(covdesc="phenodata.txt", path="data")
celfiles.gcrma <- gcrma(celfiles)

eset <- exprs(celfiles.gcrma)
eset
             GSM475246.CEL GSM019472.CEL GSM583543.CEL GSM885321.CEL GSM678897.CEL
1415670_at        8.996238      9.145484      9.042686      9.256164      9.319093
1415671_at        9.908269      9.780557      9.861036     10.114690     10.078675
1415672_at       10.435323     10.369950     10.491089     10.381307     10.524440
1415673_at        6.744400      6.698366      6.543279      6.711245      6.634974
1415674_a_at      8.027900      8.121387      7.981725      7.948881      8.070554

From there, after finding differentially expressed genes, the probe column still has no value I can call with $.

                 logFC   AveExpr         t      P.Value    adj.P.Val         B
1449015_at   -3.674883 12.439952 -46.19625 5.123217e-10 6.569675e-06 10.996695
1450276_a_at -4.343238  4.496829 -45.34939 5.835043e-10 6.569675e-06 10.953795
1418165_at   -3.909790  7.624427 -38.77655 1.753611e-09 1.316260e-05 10.543996
1416456_a_at -3.256041 10.883295 -35.44438 3.295267e-09 1.855070e-05 10.268945
1422876_at   -2.739863  3.623318 -33.10276 5.322602e-09 2.128102e-05 10.039264
1418207_at   -3.440342  4.708131 -32.80529 5.670403e-09 2.128102e-05 10.007586
1430899_at   -4.513655  5.071580 -31.48338 7.565404e-09 2.433682e-05  9.859246
1419725_at   -5.585713  7.749529 -30.63524 9.160899e-09 2.578564e-05  9.757116
1459889_at   -4.106095  4.454395 -29.81515 1.107854e-08 2.771851e-05  9.652759
1425451_s_at -3.646441 11.884753 -28.92088 1.371148e-08 3.087550e-05  9.532222

Massive thanks in advance for anyone that can help with this.

microarray bioconductor affy limma • 1.3k views
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You can use rownames to extract probe column.

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Thank you so much, it worked. I love this community so much, you never fail me.

Thank you, thank you, thank you. :)

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