How to analyze processed data from ArrayExpress?
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4.0 years ago

Hi, I have 33 ligands in total, which were analyzed through SAM. Reported in an article entitled "Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands".  I selected 10 ligands from above data and wants additional analysis but they didn't provide the RAW data/CEL, I downloaded the Processed data from "ArrayExpress". I reviewed the limma tutorial and want to make sure the downloaded data file for limma. I need a starting point for analysis through limma, I attached one of processed data file as an example, Can I use processed data files as an input for limma and which type of analysis will be performed? I will be waiting for your valuable answers. Thank you,

RNA-Seq ChIP-Seq R next-gen genome • 2.9k views
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If you have log2 normalized expression values, which they used for analysis in limma, you can import these data in limma. But read carefully on ArrayExpress what these data exactly are.

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Dear b.nota, Thank you very much. The data format are as follow

{Reporter Identifier} {RATIO} {G_PROCESSED} {R_PROCESSED}

1 [-0.148533] [42903.2] [30475.9]

........................

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A quick look into the data set, showed me that there is a lot more in GEO than that you describe here. Also unprocessed (raw) data, such as mean and median values (including their background as well).

So my advice is to first read more about microarrays, or do a quick course, and then read the limma manual in more detail, especially about how to analyze custom two color arrays.

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Did you have any success reading the processed data in using the bioconductor::ArrayExpress package?

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