Extracting microarray data - What programs do you use? (Apr/02/2008 )
We're doing Chip-chip using Agilent slides and have been (attempting) to use the Feature Extraction program to get our results after we scan our slides. We met a random in the hallway not long ago and after chatting have discovered they use a different program because "Feature Extraction" is crap.
What are your experiences? What programs are you using to extract data?
Thanks in advance!
we're using "feature extraction" v.9.5.3 and it works perfectly (as long as you have the correct grid pattern), at least for cgh and gene expression.
We have the correct grid pattern, and have even made our own (using the grid mode feature). That looks fine. But after we extract and look at the QC report, one of the corners always seem to be out of whack! We are using v.9.5.1.
did you look at the image of the scan?
when we see problems with the data (including any corner problems) it is because of a problem that shows up in the scan. it's not a software issue.
keep in mind that the qc report highlights the corners.