[BioC] asking with problems with affymetrix data

Sean Davis sdavis2 at mail.nih.gov
Fri Oct 3 13:43:18 CEST 2008

On Fri, Oct 3, 2008 at 6:52 AM, manzofabio at libero.it
<manzofabio at libero.it> wrote:
> Hi everybody,
> I'm fabio and I'm trying to analyze some affymetrix data, taken by GEO repository. Series GSE10896.
> I downloaded all the .cel file and with the affy package I read them in R. Then I applied the MAS5 algorthm. The data normilized, I gave a look to the inspective plots (boxplot, MA-plot) and they seem fine. Then I applied the limma to discover differentially expressed genes, but I didn't find anything. The authors applied a wilch test, and so I took the data normilized and I put them in MEV. I applied the wilch test with p.value = 0.05. Then I put them in fold change, but...I didn't find any differences, while the authors 108 genes higher then 1.2. Can someone tell me which mistake I'm doing?

It is not unusual to get different results when re-analyzing data.
That said, without seeing the code that you have used and your
sessionInfo(), it is hard to tell if there are obvious problems.  You
can certainly post your code here to get feedback, but, ultimately, if
you feel that your answers differ from the original paper, you may
want to contact the authors for more details.


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