Which statement is NOT a common assumption in microarray experiments?

Which statement is NOT a common assumption in microarray experiments?

• A. Cross-hybridization cannot occur.
• B. Probe specificity is assumed to be perfect.
• C. Normalization across arrays is unnecessary.
• D. Inability to detect novel transcripts or isoforms.

Answer: (D)

Microarray experiments rely on hybridizing labeled transcripts to predefined probes on a chip, so the interpretation rests on certain practical assumptions: each probe reports its target transcript with high specificity, cross-hybridization is minimized, and data across arrays can be normalized to make samples comparable. These assumptions drive how the data are analyzed and interpreted. The statement about being unable to detect novel transcripts or isoforms is not an assumption researchers usually rely on. Instead, it’s a limitation of microarrays: since probes are designed for known sequences, they generally cannot discover new transcripts or unannotated isoforms unless those sequences were represented by existing probes. If you need to find novel transcripts, sequencing-based approaches like RNA-seq are used. The other ideas reflect common design assumptions: probes are specific to their targets, cross-hybridization is kept to a minimum, and normalization across arrays is typically used to correct technical variation.

Microarray experiments rely on hybridizing labeled transcripts to predefined probes on a chip, so the interpretation rests on certain practical assumptions: each probe reports its target transcript with high specificity, cross-hybridization is minimized, and data across arrays can be normalized to make samples comparable. These assumptions drive how the data are analyzed and interpreted.

The statement about being unable to detect novel transcripts or isoforms is not an assumption researchers usually rely on. Instead, it’s a limitation of microarrays: since probes are designed for known sequences, they generally cannot discover new transcripts or unannotated isoforms unless those sequences were represented by existing probes. If you need to find novel transcripts, sequencing-based approaches like RNA-seq are used.

The other ideas reflect common design assumptions: probes are specific to their targets, cross-hybridization is kept to a minimum, and normalization across arrays is typically used to correct technical variation.