Tried processing Human Gene 2.0 files manually using expression console

[cbat...@uottawa.ca]

Hello,
I have tried processing Human Gene 2.0 files manually using expression
console but still an error message where the code went as follows:

Beginning to Process the Hs gene dataset

19631 Ensembl GO/pathway annotations imported in 3 seconds
25516 constitutive genes and 237320 array IDs imported out of 237321 lines.
Exon data imported in 0 seconds

[Errno 22] invalid mode ('w') or filename:
u'C:\\Users\\User\\Desktop\\AltAnalyze_v.2.0.7-Win64\\arrays.C:/Users/User/Desktop/cel/rma-gene-full.summary.txt'


Any ideas how to resolve?

Thank you very much for your help.

Best
Cory

[Nathan Salomonis]

Hi Cory,

So sorry for the very late reply! I'm not exactly sure what is used as input in the below example for AltAnalyze. Did you already run ExpressionConsole separately before this to get transcript-cluster level results? Did you try running AltAnalyze as I recommended in the previous email on your CEL files to get the probeset-level expression data (will crash though as indicated in that thread but will give you an expression file).

When running APT manually, I recommend downloading from:
http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx

and seeing the instructions for running from here:
http://www.affymetrix.com/support/developer/powertools/changelog/apt-probeset-summarize.html

When analyzing these arrays you want to run with the options -p -c -b -a -o --cel-files
For -a I include -a "rma-sketch" -a dabg

This is a bit different from running in AltAnalyze which is what it shown in your run immediately below. Expression Console is a windows based application form Affymetrix which should also do the above using a nice GUI interface rather than command-line.

Best,
Nathan