High Variation Of Raw Intensities In Same Transcript Cluster In Gene Expression Array

Without background correction and normalization, the spots of the same gene expression array have very high intensity variation on probe level. For example, the raw intensities on HuGene-1st-v1 (triplicate) the gene MSI2 vary between ~5300 and 27 for the same gene:

probeID    array1    array2    array3     chr      strand    start      stop         transcript_cluster_id
8008692    5374         4372       3524          chr17       +         55674267    55674299     8008682
8008698       37         30           27          chr17       +         55752413    55752455     8008682

Is this normal? Thank you.

affymetrix probeset

• 2,129 views • link

updated 13.0 years ago by Devon Ryan

• written 13.0 years ago by munch •

1 answer

Those two probes have only partial overlap in the transcripts that they cover, so I can't say I find that surprising.

• 275 views • link

written 13.0 years ago by Devon Ryan