APT error in Alt Analyze

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Lawrence McKinney

Oct 28, 2019, 9:39:05 PM10/28/19
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Im trying to run analysis on Affymetrix Yeast data. I followed all of the instructions. After I set my groups I ran tried to run the analysis. The error below pops up immediately. I tried to troubleshoot and looked at the blog to see how others tried to resolve the issue. I made sure my permissions allowed APT files (apt-midas and apt-probeset-summaries) to read and write. Also, there is no file for APT in my Expressioninput folder in the output directory. 

Operating system - MacOS
Altanalyze version - 2.1.3

Can you assist?

Thank you, 


Beginning AltAnalyze Analysis... Format: log
AltAnalyze version 2.1.3 - Expression Analysis Parameters Being Used...
database: EnsMart72
species: Sc
method: 3'array
manufacturer: Affymetrix
probability_statistic: moderated t-test
constitutive_source: Affymetrix
dabg_p: NA
raw_expression_threshold: NA
avg_all_for_ss: no
expression_data_format: log
include_raw_data: no
run_from_scratch: Process CEL files
perform_alt_analysis: NA
calculate_gene_expression_using: constitutive
Alternative Exon Analysis Parameters Being Used...
analysis_method: NA
p_threshold: NA
filter_data_types: NA
alt_exon_fold_variable: NA
gene_expression_cutoff: NA
remove_intronic_junctions: NA
avg_all_for_ss: no
permute_p_threshold: NA
perform_permutation_analysis: NA
export_NI_values: no
run_MiDAS: no
use_direct_domain_alignments_only: no
microRNA_prediction_method: any
analyze_all_conditions: pairwise
filter_for_AS: no
run_GOElite: run-immediately
Processor architecture set = 64bit x86_64
Beginning probeset summarization of input CEL files with Affymetrix Power Tools (APT)...
Trying to change APT binary access privileges
Traceback (most recent call last):
  File "AltAnalyze.pyc", line 5417, in AltAnalyzeMain
OSError: [Errno 2] No such file or directory: '/Applications/AltAnalyze/AltDatabase/affymetrix/APT/Mac/apt-probeset-summarize'

Nathan Salomonis

Oct 28, 2019, 9:50:57 PM10/28/19
to alt_pre...@googlegroups.com
Hi Lawrence,

AltAnalyze supports a number of array formats for Affymetrix, but support for new formats and specialized arrays types have not been updated in the last 6 years (90% of development focused on RNA-Seq analyses). My guess is that this is a new array format they had a different file format than CDF libraries for processing the cells, or CLFs that require some additional configurations. 

Nonetheless, if you get quantification results, AltAnalyze can accept standard tab-delimited input files (e.g., RMA normalized) and process those in an automated manner for all major analyses.


On Oct 28, 2019, at 9:39 PM, Lawrence McKinney <lmckin...@gmail.com> wrote:


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