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Microarray data analysis pipeline

I want to analyse microarray data in R language. I have .txt files taken from NCBI GEO database. I have gone through different sites which contain R scripts consisting of CEL files. Can please anyone tell me how to process the text files using R script? The text files contains ID, adjusted P-value, P-value, t, B, logFC value and gene names. Thanks in advance

microarray
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written by smrutimayipanda • smrutimayipanda

if I have CEL files then how can i go through the procedures? at last, I need an expression matrix. How should i proceed with the CEL files?

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written by smrutimayipanda • smrutimayipanda

1 answer

Evidently, you have downloaded results tables that relate to one or more differential expression comparisons, and that you have not downloaded any raw data. So, there is no more processing that you need to do with these files other than to interpret the results. If you are not even sure to what these results tables relate, then I suggest that you discuss this matter with a person locally, such as a co-worker, your supervisor, or some other colleague or collaborator.

If you want help to re-process the data from the raw stage, then I suggest that you first obtain the raw data. These will be different depending on the platform:

  • Affymetrix: CEL
  • Agilent: TXT (but not the TXT files that you have)
  • Illumina: IDAT

You could also let us know the GSE number of the dataset of interest.

Kevin

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written by Kevin Blighe Kevin Blighe

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