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

Question

[munch]

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.

Answer 1

[Devon Ryan]

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