how to check which probesets belong to which transcript?

Imn first time working on microarray data analysis. My chip is hugene 2.0 ST. Using xps package I have differential expressed exons.

   Probeset ID UNIT_ID Statistics    Mean1    Mean2 StandardError DegreeOfFreedom
    16657437    3742   -3.87699  1.80551  8.27607      0.566558               4
    16657441    3745    2.89796  3.81905  1.38638      0.504455               4
    16657456    3757    3.14543  4.51182  1.69900      0.447957               4
    16657519    3802   -3.04069  5.91567 18.16170      0.532210               4
    16657589    3857   -2.97385  4.26765 10.45620      0.434738               4
    16657604    3867   -3.26664 21.48650 37.10300      0.241258               4
   Probeset ID  P-Value P-Adjusted FoldChange
    16657437 0.0178869  0.0178869   4.583780
    16657441 0.0442085  0.0442085   0.363018
    16657456 0.0346659  0.0346659   0.376568
    16657519 0.0383762  0.0383762   3.070100
    16657589 0.0409876  0.0409876   2.450110
    16657604 0.0308867  0.0308867   1.726800

In the above table the probeset Id represents differential expressed exons. So now, How to check which probesets belong to which transcript? Thank you in advance.

microarray affymetrix hugene2.0st data

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updated 10.4 years ago by Amitm

• written 10.4 years ago by Vasu

1 answer

hi, One way to get the annotation is to go to Affymetrix website and download the annotation file from their downloads section - enter image description here

Download the Probseset annotation CSV file. The file is garangtuan though when opened in excel (unless you are ok with parsing it using any sort of scripting). A quick fix solution would be to go to the NetAffx annotation centre on Affy website again. enter image description here

Here you can query your probeset IDs and get annotation. The last time I checked, the limit of batch query was 5000.

• 2 views • link

written 10.4 years ago by Amitm