changing feature names (row names) for expressionset object?
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2.7 years ago
RNAseqer ▴ 200

Hello everyone,

Has anyone had experience changing the rownames of the expressionset (the intensity matrix) for an affy expression-set object?

Somehow mine got changed from probe IDs to simple numbers (1 for the first probe, 2 for the second etc.) and I'd like to change them back.

> exprs(raw_data3)
VV51m.CEL VV50m.CEL VV38m.CEL VV39m.CEL VV64m.CEL VV41m.CEL VV42m.CEL
1             81       112        78       126        89       151        76
2          26040     26340     37500     23806     17441     24346     24528
3            223       139       181       137       115       215       256
4          26636     27397     37258     25243     17756     25380     24787
....

expressionset limma rownames • 1.4k views
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rownames() is the command...

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As per ATpoint, if the object is genuinely an ExpressionSet, you just need to do rownames(raw_data3). This will then change all rownames throughout the entire object's contents.

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Thanks! That is good to know. It seems as though this was fixed automatically a step or two later in the pipeline by the rma function. After rma the rownames do appear to be probe IDs again.

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What was your command for generating raw_data3?

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> raw_data3 <- oligo::read.celfiles(filenames =
"VV51m.CEL",
"VV50m.CEL",
...
)