Z-score for human-microarray and mouse ish-data

Hi,
the human micro-array data provides the z-score and according to
http://help.brain-map.org/display/humanbrain/API
“* a vector of z-score values in the same order as the “samples” array. Note: z-score is computed independently for each probe over all donors and samples.”
i re-calculated the z-score for each probe with this formula, but i am unable to obtain the same z-score-values as provided in the dataset:
(expression_level - expression_level.mean())/expression_level.std()

I obtained data using this rma-query:
http://api.brain-map.org/api/v2/data/query.json?criteria=
f"model::Probe,rma::criteria,gene[acronym$il{self.geneAcronym}],rma::options[num_rows$eqall],"
“pipe::list[probes$eq’id’],”
“service::human_microarray_expression[probes$eq$probes]”

You can get the expression-levels and z-scores for the second probe here:
https://drive.google.com/open?id=1e3bBJGT-gX7eElDbKe1blXDpV-D07Cxs

how do I correctly calculate the z-score on behalf of this data?

some background: we are trying to compare z-scores for human-microarray data with mouse ish-data , which is unfortunatelly not providing z-scores. alternatively: how can we obtain z-scores for ISH using the api/sdk that are consistent with the z-scores from microarray-data?

thanks and regards
Christoph

Hi @christoph-hue, Z scoring of the microarray data has already been address in this community forum post. Can you take a look at that and reply to this thread if it does not address your issue? I don’t know how to calculate Z scores in the mouse ISH data so if that ends up being necessary, someone else will need to reply.

hi @jeremyinseattle , I’ve already read it but it doesn’t really address the issue. my questions basically are: can I calculate the z-scores provided for one probe using the expression-levels of this probe and if so, how? because I don’t get the same values with the formula stated here: What is the Z score reference value in RNAseq GBM data?
you might want to clarify what the x is in your formula, in case it isn’t the expression-level (which I assumed). thanks!

If the Z score formula still doesn’t work, it may be the difference between downloading the data at the level of samples vs. structures. Can you try following this steps from this post for downloading the data at the sample level and then calculating the Z scores to see if you get the expected answer? You are correct that “x” is the vector corresponding to expression levels for a given probe when calculating Z scores. If this still doesn’t solve your problem, or if you would prefer to use the API, please post again and I’ll see if I can find someone else to address the question.