On Jan 2, 2008 12:31 PM, affy snp <affysnp@gmail.com> wrote:

> Hello, dear list:
>
> I recently had questions about Illumina data two months ago because of
> a large portion of negative values found. Suggested by some expertises
> here, I requested our microarray facility to re-process the data by not
> doing
> any global or background subtraction etc. This way, in deed, there is no
> negative values existing. But very surprisingly, by applying two packages,
> Lumi and Beadarray respectively, after normalization, the fold change
> between the test and normal samples is around 1. Apparently, it should
> not be this case. Can anybody here offer some possible reasons for this?
>

Hi, Allen.

Do you mean that there are no differentially expressed probes?  What test
did you do (limma, t-test, etc.)?  And what information suggests that "it
should not be the case"?

If there are not differentially expressed probes, there could be many
reasons, both biological and technical for this being the case.  You will
probably need to dig into the data to check the quality closely.  Also, make
sure that sample labels were not switched, etc.  In short, when you get a
result that you don't expect, you will need to do some troubleshooting and
if you come up empty (no technical explanation), then you (unfortunately)
need to explain to your lab collaborators (or yourself) that the experiment
did not show differences.

Hope that helps,
Sean

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