If you want to evaluate one gene expression, i would use a positive and negative control which is cell line that is known of expression of your gene. also i would use absulate expression rather relative expression using qPCR. i hope this answer make sense for you

Hi Juan

Massar gave you very good advice since you can't compare qPCR data with expression data made with arrays. Technologies, conditions, type of samples (different culture, treatment, harvest, RNA extraction...) and Biases are so different that you will mis-analyze.

do you have the possibility to choose one sample to take as a gold standard?

fred

Hi Juan,

How rigorous do you need the comparison? While I agree with the above statement regarding comparisons made between platforms (qPCR, microarray, RNA-seq), you should be able with reasonable confidence if you compare to a known housekeeping gene. Such a standardization would help you deal with the variables associated with your choice of platform (polymerase efficiency, temperatures, cDNA amount/quality, etc...).

If you need a gene expression database, I prefer the Gene Expression Omnibus from the NCBI (https://www.ncbi.nlm.nih.gov/geo/), which is the repository of essentially all genome-wide datasets funded by NIH grants. Also, EMBL-EBI has an 'atlas' for expression levels across tissues/conditions, but I use this less (https://www.ebi.ac.uk/gxa/home).

Thank you guys! All of you are right, many thanks :)

Thank you Massar and of course you are right but what I had at this moment it was that experiment results using qPCR. It is a good idea try to rethink the whole process again and see if it would be worth it analyze it as absolute.

Frederic I don't want really make comparisons, I know is not possible to compare and merge this type of data but maybe take a reference and kind of have a little sight of where is the expression in terms of high / low. In this case we are characterizing for the first time so we want to know approximately where are the expression in a gross view.

And thank you Mark, since I am not looking for a very rigorous data I will try to see if with a reference I can see where are we standing on the big picture, that for us and for now it would be enough. Thanks for the database linnks I was searching on Omnibus already and in some others, I will priorize Omnibus and check Atlas as well, that is helpfull to narrow the searches, there is a lot of banks and databases over there now...

Many Thanks again guys :)

if you go to TCGA cbioportal you can find all the RNA seq and mutations of about 1000 lines in the Novartis -Broad collection