A method of determining mislocalization of an analyte, wherein the analyte is RNA, within a biological sample, the method comprising: (a) aligning the biological sample with an array; (b) obtaining a first image of the biological sample; (c) actively or passively transferring the analyte from the biological sample to the array and hybridizing the analyte to a capture domain of a capture probe on the array, wherein the array comprises a plurality of capture probes, wherein the plurality of capture probes comprise a capture domain; (d) extending the capture probe using the analyte as a template, thereby generating an extended capture probe; (e) hybridizing a padlock probe or a snail probe to the extended capture probe; (f) circularizing the padlock probe or the snail probe; (g) amplifying the padlock probe or the snail probe, thereby generating an amplified circularized padlock probe or an amplified circularized snail probe; (h) hybridizing a plurality of detection probes to the amplified circularized padlock probe or the amplified circularized snail probe, wherein a detection probe from the plurality of detection probes comprises: a sequence that is substantially complementary to a sequence of the padlock probe or the snail probe, or a complement thereof, and a detectable label; (i) obtaining a second image of the biological sample and detecting a signal intensity from the plurality of detection probes in the second image; and (j) determining mislocalization of the analyte within the biological sample by comparing the first image of the biological sample to the second image of the biological sample. (a) aligning the biological sample with an array; (b) obtaining a first image of the biological sample; (c) actively or passively transferring the analyte from the biological sample to the array and hybridizing the analyte to a capture domain of a capture probe on the array, wherein the array comprises a plurality of capture probes, wherein the plurality of capture probes comprise a capture domain; (d) extending the capture probe using the analyte as a template, thereby generating an extended capture probe; (e) hybridizing a padlock probe or a snail probe to the extended capture probe; (f) circularizing the padlock probe or the snail probe; (g) amplifying the padlock probe or the snail probe, thereby generating an amplified circularized padlock probe or an amplified circularized snail probe; (h) hybridizing a plurality of detection probes to the amplified circularized padlock probe or the amplified circularized snail probe, wherein a detection probe from the plurality of detection probes comprises: a sequence that is substantially complementary to a sequence of the padlock probe or the snail probe, or a complement thereof, and a detectable label; a sequence that is substantially complementary to a sequence of the padlock probe or the snail probe, or a complement thereof, and a detectable label; (i) obtaining a second image of the biological sample and detecting a signal intensity from the plurality of detection probes in the second image; and (j) determining mislocalization of the analyte within the biological sample by comparing the first image of the biological sample to the second image of the biological sample.