APT error in Alt Analyze

[Lawrence McKinney]

Hi, 

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, 

Lawrence

————————

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]

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.

Best,

Nathan

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

Hi, 

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