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content/post/2008-02-28-follow-up-on-meta-analysis.markdown

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+---
+author: einar
+categories:
+- Science
+comments: true
+date: "2008-02-28T19:42:15Z"
+header:
+  image_fullwidth: banner_other.jpg
+slug: follow-up-on-meta-analysis
+tags:
+- meta-analysis
+- microarray
+- Science
+title: Follow up on meta-analysis
+disable_share: true
+wordpress_id: 378
+---
+
+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.
+
+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.
+
+According to the documentation, the "merge" command should be used to deal with these cases, but here's what I get:
+
+{{< highlight R >}}
+
+>> RG1 = read.maimages(file="file1.txt",source="smd")
+Read file1.txt
+>> RG2 = read.maimages(file="file2.txt",source="smd")
+Read file2.txt
+>> merge(RG1,RG2)
+Error in merge(RG1,RG2): Need row names to align on
+>> rownames(RG1)
+NULL
+>> rownames(RG2)
+NULL 
+{{< / highlight >}}
+
+I'm going to ask the Bioconductor ML and see what they tell me.