DEG analysis for Micro array affymetrix
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@sheikhbeigali-22924
Last seen 15 months ago

Hello to all, I have expression data from micro array affymetrix, i want to analysis the DEG could you help which R package is suitable for DEG analysis and also tell me a tutorial and script step by step because am beginner in this filed.

Thanks for your help

Ali

DEG • 329 views
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@kevin
Last seen 1 hour ago
Republic of Ireland

Hey Ali, it would help if you elaborated on the data that you currently have - presumably, you have obtained CEL files, but, do you know which specific array platform and version it is? Knowing the platform is important due to the fact that the Affymetrix arrays differ in their design. For example, some platforms cannot be pre-processed with the traditional affy package, and instead require the oligo package; however, oligo should now cater for all Affymetrix array designs and, for all intents and purpose, be the sole package used.

A general workflow proceeds as follows:

  1. Data import, pre-processing, and QC (primarily oligo)
  2. Differential expression analysis (limma)

A pretty good end-to-end workflow can be found here:

Other useful resources:

Kevin

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Dear Kevin, Appreciated for your helpful guide, The array platform is "[OElncRNAs520855F] Affymetrix Human Custom lncRNA Array", in my task, i can imported the data now the problem is about annotation, please could guide me how is possible to annotate these data from this platform? I would be appreciated for your guide Ali

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Hey, no problem. I am not too familiar with this custom lncRNA array ('chip'). Do you have access to the annotation file? - there seems to be a copy on GEO, here:

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