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| author | comments | date | layout | slug | title | wordpress_id | categories | header | tags | ||||||
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| einar | true | 2008-02-28 19:42:15+00:00 | page | follow-up-on-meta-analysis | Follow up on meta-analysis | 378 |
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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.
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 {% endhighlight %}
I'm going to ask the Bioconductor ML and see what they tell me.