Luca Beltrame
64b24842b8
All checks were successful
continuous-integration/drone/push Build is passing
40 lines
1.4 KiB
Markdown
40 lines
1.4 KiB
Markdown
---
|
|
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
|
|
omit_header_text: true
|
|
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.
|