[Errno 22] invalid mode ('w') or filename: u

[SP]

I am trying to run an analysis with affymetrix mouse exon array data that has been normalized outside AltAnalyze. The input file is a text file containing normalized, batch corrected data from 6 treatment samples (condition 1) and 5 control samples (condition 2). The p value file is the dabg output file from Affymetrix Expression Console (as suggested by the AltAnalyze wiki). The data file contains the core probeset. Running AltAnalyze with default parameters gives me the above error. What am I doing wrong?

 

Thanks,

SP

[Nathan Salomonis]

Hi SP,

Can you send the log file produced by AltAnalyze. This will be in your designated output directory. Off hand I know of no immediate reasons while AltAnalyze would fail. Our typical workflow considers all probesets initially and filters based on options provided in the program to core or other (we actually reannotate these based on the latest mRNA alignment data for each database). 

If you don't feel comfortable sending the log file, you can run your original arrays in AltAnalyze and the format of the resulting input expression and stats files to the ones you obtained through batch effects normalization. It is probably a formatting issue (should be tab delimited text files with a single header row and a probeset ID annotation column).

Best,

Nathan

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[SP]

Hi Nathan,

 

    Sorry for the delay in replying. The log file text is pasted below. For IP reasons, I have removed the files and directory names. FYI, I am running AltAnalyze on a Windows 7 SP1 machine with an Intel Xeon processor and 12 GB of RAM.

 

 

    ------- Log File Text-------

 

Beginning AltAnalyze Analysis... Format: log
AltAnalyze version 2.0.7 - Expression Analysis Parameters Being Used...
 species: Mm
 method: exon
 manufacturer: Affymetrix
 probability_statistic: Kolmogorov Smirnov
 constitutive_source: Ensembl
 dabg_p: 0.05
 raw_expression_threshold: 1.0
 avg_all_for_ss: no
 expression_data_format: log
 include_raw_data: yes
 run_from_scratch: Process Expression file
 perform_alt_analysis: yes
 calculate_gene_expression_using: constitutive
Alternative Exon Analysis Parameters Being Used...
 analysis_method: splicing-index
 p_threshold: 0.05
 filter_data_types: core
 alt_exon_fold_variable: 2.0
 gene_expression_cutoff: 3.0
 remove_intronic_junctions: NA
 avg_all_for_ss: no
 permute_p_threshold: 0.05
 perform_permutation_analysis: NA
 export_NI_values: no
 run_MiDAS: yes
 use_direct_domain_alignments_only: inferred comparison
 microRNA_prediction_method: any
 analyze_all_conditions: pairwise
 filter_for_AS: no
 run_GOElite: decide_later
Beginning to Process the Mm exon dataset
22659 Ensembl GO/pathway annotations imported in 3 seconds
28154 constitutive genes and 669464 array IDs imported out of 669465 lines.
Exon data imported in 4 seconds
[Errno 22] invalid mode ('w') or filename: u'D:\\Programs\\AltAnalyze_v.2.0.7-Win64\\arrays.D:/Data/XXX/ComBat_Correction/AltAnalyze_03July2012/493 Results/combat.XXX.txt'

 

------- End Log File Text ----------

[Nathan Salomonis]

Hi SP,

Although the last line would indicate the program is having an issue resolving the destination path on your machine, the file that it is trying to write is written when your groups. file does not correspond to your exp. column in terms of the column names provided. This should only happen when you are running altanalyze in command-line mode since the GUI will create a groups. file automatically without mistakes.

If using the GUI, let me know since this means I'm on the wrong track with QCing this. Otherwise, if you are using the command-line mode or have created your groups. file outside of AltAnalyze (which you don't need to do when running the GUI) then check your column headers in both and make sure they correspond exactly. I will see what issues there is with the arrays. file being output that are shown below (this file is written to say what names in groups. might be wrong).

Best,

Nathan

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[SP]

Hi Nathan,

 

     I am running the GUI and not the command line version of the program. I had actually tried creating a groups. and a comps. file in the data directory, the GUI automatically takes those files and creates the groups. However, it gives me the same error.

 

Thanks,

SP

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[Nathan Salomonis]

Hi SP,

you will need to delete the manually created groups and comps folder in the destination directory under the folder ExpressionInput, otherwise, AltAnalyze will still use these relationships. If you delete these, create groups and comps through the GUI and then still get the error please let me know.

Best,
Nathan

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[SP]

Hi Nathan,

 

     I have done that. I am still getting the same error.

 

Thanks,

SP