39 lines
1.4 KiB
Markdown
39 lines
1.4 KiB
Markdown
---
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author: einar
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comments: true
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date: 2008-02-28 19:42:15+00:00
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layout: page
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slug: follow-up-on-meta-analysis
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title: Follow up on meta-analysis
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wordpress_id: 378
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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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Fourteen days since my last post. Quite a while, indeed. Mostly I've been stumbled with work and some health related issues. Anyway, I thought I'd follow up on the meta analysis matter I discussed in my last post.
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It turns out that it's a fault of both limma and the data sets, because apparently the raw data found in the Stanford Microarray Database have different length, gene-wise (a result of not all spots on the array being good?) and limma itself does need equal length tables to form a single object (I stumbled upon the same problem when doing my thesis, but I used a hack to work around it), and does not perform any checking.
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According to the documentation, the "merge" command should be used to deal with these cases, but here's what I get:
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{% highlight R %}
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>> RG1 = read.maimages(file="file1.txt",source="smd")
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Read file1.txt
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>> RG2 = read.maimages(file="file2.txt",source="smd")
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Read file2.txt
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>> merge(RG1,RG2)
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Error in merge(RG1,RG2): Need row names to align on
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>> rownames(RG1)
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NULL
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>> rownames(RG2)
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NULL
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{% endhighlight %}
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I'm going to ask the Bioconductor ML and see what they tell me.
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