25 lines
1.5 KiB
Markdown
25 lines
1.5 KiB
Markdown
---
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author: einar
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comments: true
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date: 2008-02-14 20:17:09+00:00
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layout: page
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slug: meta-analysis-difficulty-increasing
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title: Meta analysis difficulty increasing
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wordpress_id: 377
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categories:
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- Science
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header:
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image_fullwidth: "banner_other.jpg"
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tags:
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- meta-analysis
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- microarray
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- Science
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---
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Again in the past days I've been banging my head thanks to the fact that doing meta-analysis with microarray data is more difficult than what it seems.
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The problem sometimes lies in the data, sometimes lies in the analysis software and sometimes in a combination of factors. When doing work on a public data set (Zhao et al., 2005), I had to start analysis from raw data. Now, I tried using both the limma and marray Bioconductor packages, but both of them bail out with cryptic error messages. From what I've learnt by googling around, it seems that R doesn't like batch loading of tables of different length.
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I have 177 samples and I **have** to normalize them all together. Apparently this is a quirk of marray and limma (or worse, R itself) which is preventing me to work properly. And this is not the first time it happens, either: in the past year I've lost a lot of time dealing with software issues rather than performing real analsis. The problem has been posted already on some R mailing lists (and on BioC, too), but judging from the responses I doubt I'll see a solution.
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I guess I'll have to work around this somehow (and of course, this doesn't improve the idea I have of R...).
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