AltAnalyze Frequently Asked Questions

Main Analysis Options

• What operating systems is AltAnalyze compatible with?
• Can I run AltAnalyze on a remote machine without using the graphical user interface?
• How can I visualize splicing and domain level changes from AltAnalyze?
• What microarrays can AltAnalyze work with?
• Can AltAnalyze work with exon/junction data for an unsupported platform (e.g., custom array)?
• What is the difference between the splicing-index, FIRMA, MiDAS, Linear Regression and ASPIRE methods?
• How can I annotate my splicing results from another program in AltAnalyze?

Installing AltAnalyze

• Why Does AltAnalyze crash when trying to download the database when first run?

Data Analysis and Import

• What files do I need when analyzing Affymetrix arrays?
• When I have dozens of samples in my study, how can I more easily assign the samples to groups than one by one?
• What is the recommended cutoff for expressed genes with RNA-Seq?
• Why does AltAnalyze need to filter my data?
• Should I calculate gene expression using constitutive or all mRNA aligning probests?
• How does a pair-wise alternative exon analysis differ from multiple group comparisons?
• Why do I need to define groups and comparisons?
• Why doesn't AltAnalyze run GO-Elite by default?
• Why does AltAnalyze download the Gene 1.0 transcript annotation file for Exon 1.0 array analyses?
• How can I remove probesets with sequence that aligns to multiple genomic loci from my analysis?
• Can AltAnalyze return transcript cluster results instead of Ensembl for the Gene 1.0 array?

Probeset Alignments and DomainGraph

• How do AltAnalyze probeset-to-gene and probeset-to-exon mappings differ from those in the Affymetrix annotation files?
• In AltAnalyze a probeset associated with an intron is predicted to alter protein domain composition of the protein, but in DomainGraph why don't I see the probeset?
• How do I start DomainGraph and what can I do in DomainGraph?

Interpreting Alternative Exon Results

• Why don't the folds and expression values from my RNA-seq experiment don't seem to match correctly?
• What is a constitutive exon/junction?
• Which results should I validate?
• If two probesets align to one exon and have opposite splicing changes, what does this mean?
• What does the (+) and (-) mean proceeding a protein domain, miRNA binding site or protein identifier?
• What does the identifier E2-3 indicate and where does this annotation come from?
• Where do the alternative splicing annotations provided in the column "exon annotations" come from?
• What does the column "distal exon-region-ID" indicate?
• What is the adjusted fold versus the non-adjusted fold change?
• Why do all alternative exons have the indicator "exon-inclusion" in the column "event_call"?
• How can I graph my splicing scores for all exons in a gene?
• What is the difference between exon-level and gene-level alternative exon results?
• When viewing AltAnalyze results in DomainGraph, why don't the identifiers match to my array/RNA-seq platform?

Other

• Who are you and what's your deal?