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Question: How to Normalize the Microarray Data Obtained from ncbi?
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gravatar for pankajnarula84
3.4 years ago by
India
pankajnarula8420 wrote:

I have micro array data in GSE format from http://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE1739. My simple question is how to normalize this data ? All I could see was gene symbols and IDs. I could not find numbers to normalize (As my background is Mathematics, very poor knowledge about gene data). I know there is one R package `limma` with function `normalizeWithinArrays`. But no idea how to implement on the data set mentioned above. Please provide some insight. Thanks in advance.

ADD COMMENTlink modified 3.4 years ago by James W. MacDonald47k • written 3.4 years ago by pankajnarula8420

You can try to download the raw data files. Then you can use any type of normalization method you like the best.

ADD REPLYlink written 3.4 years ago by b.nota300
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gravatar for James W. MacDonald
3.4 years ago by
United States
James W. MacDonald47k wrote:

While using geo2r is helpful for doing analysis on the web, if you want to analyze data within R, you should use the GEOquery package.

Also note that these data are from the Affymetrix Human Focus array, so you don't want to process using limma. Instead you want to use the affy package. In addition, this is an old data set and they used MAS5.0 to summarize, rather than something more reasonable like RMA, so you are likely to be better off getting the raw data and summarizing yourself.

If you have very poor knowledge about gene data you should either inform yourself or find a collaborator who does have that knowledge. As a first step in informing yourself, you could start here.

ADD COMMENTlink written 3.4 years ago by James W. MacDonald47k
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