Data Analysis with Agilent Microarray RNA Seq Files

Question

[Adisa Trnjanin Hadzic]

Does anybody has an understandful guidance/instruction how to analyze .txt files from Agilent Microarray RNA Seq? This old files are from 2008 and I need to know which genes are over- and which under-expressed. I read that I have to use the gProcessedSignal value to analyze but I have really no clue where to start nor what to do first... I am thankful for any advice regarding this points. Here you can se some of the data the text files contain:

TYPE    integer integer integer integer integer text    text    float   float   float   float   float   float   float   boolean
FEATURES    FeatureNum  Row Col SubTypeMask ControlType ProbeName   SystematicName  PositionX   PositionY   gProcessedSignal    gProcessedSigError  gMedianSignal   gBGMedianSignal gBGPixSDev  gIsSaturated
DATA    12  1   12  0   0   A_52_P616356    NM_009912   677.839 264.071 2.81    2.80E+00    28  17  
DATA    13  1   13  0   0   A_52_P580582    NM_008725   702.973 263.73  29.67   4.08E+00    53  17  
DATA    14  1   14  0   0   A_**strong text**52_P403405 NM_007473   729         263.455 7.33    2.91E+00    33  17  
DATA    16  1   16  0   0   A_51_P331831    NM_0010424  779.28  263.333 67.10   7.28E+00    86  
DATA    18  1   18  0   0   A_51_P430630    NM_008159   830.5   263.5   2.86    2.85E+00    27.5    18

Answer 1

[Benn]

Agilent microarrays are something else than RNAseq. It is both gene expression analysis, but microarrays are not sequencing.

Best way to analyze microarrays is with limma in R. There is a very good manual, also describing analysis with Agilent arrays. Good luck!

[Adisa Trnjanin Hadzic]

Thanks b.nota, yes made surely a confusion between microarray and rna seq, thanks! There is an online manual guide for Limma R that I know, but are there any online tutorials as well that could help?

[Benn]

There are also online tutorials available, of course, but the the limma manual is pretty helpful for beginners. It helped me a lot, when I started with it (long ago).

[Adisa Trnjanin Hadzic]

Thank you very much for your answer! I will definitely try it with Limma R. Best, Adisa