Hi.

Sorry about the off topic (not bioconductor) question but with so many statisticians and microarray users on the list I hoped it would be a good place to post.

I am new to microarray work and we have clinical samples we would like to run on Affymetrix chips. The RNA looks good by various analysis but the amount of cRNA from many of the samples is suboptimal. 

My question is this: can we compensate for using different amounts of cRNA at the analysis stage e.g. using a scaling factor or other means? For instance if one chip ran with 15ug cRNA and another with 7ug can this be accomodated sensibly or would the comparison of these two chips be essentially meaningless?

Thank you for any advice.

Iain

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