Comments on: Three reasons to distrust microarray results

By: Randomise your samples! « I Love Symposia!

Randomise your samples! « I Love Symposia! — Fri, 19 Dec 2008 05:49:35 +0000

[...] Tags: biology, biotechnology, experimental design, statistics trackback Microarrays certainly get a lot of flak for being noisy sources of data. It’s certainly a valid concern, since a single microarray [...]

By: Carl

Carl — Thu, 18 Dec 2008 00:47:57 +0000

This hasn’t been my experience it all. I should mention firstly that I use exclusively expression-based microarray methodologies, so I can’t speak about other platforms. We don’t simply report p-values. Instead, we use FDR-corrected q-values. Of the genes that change the most, we only rarely find false positives, and when we do, it’s usually because probe annotations in public databases were faulty (probe actually represented some intergenic transcript, rather than the gene annotated). After hand-curating the offending probes, we can usually reproduce the data. I admit I don’t know the true degree of false negatives. In reference to reproducibility, that’s why we perform multiple n’s, principle component analyses, etc. Though, again, in my hands, most array differences arise from biological, rather than, array methodology variance. I don’t believe I’m alone in that respect, see PMID: 16964229, PMID: 18793455, for example. We’ve even had some of our studies repeated by other labs, and the lists of differentially-expressed genes, even when using a slightly different statistical analysis and different array normalization procedures, were remarkably similar.

By: Microarrays may be bad, but not that bad. « Suicyte Notes

Microarrays may be bad, but not that bad. « Suicyte Notes — Tue, 16 Dec 2008 00:14:20 +0000

[...] which involves a lot of microarray data analysis. However, a series of recent blog posts [here, here and here] talk about microarray-related problems that differ so much from my own experiences that I [...]

By: The Third Bit » Blog Archive » Three Reasons to Distrust Microarray Results

Wed, 10 Dec 2008 20:10:47 +0000

[...] Interesting post: …the paper actually demonstrated that is it possible to distinguish microarray experiments conducted on one day from experiments conducted another day. That is, batch effects from the lab were much larger than differences between patients who did and did not respond to therapy… As is so often the case, data were mislabeled. In fact, 3/4 of the samples were mislabeled. [...]