Hello,

I used GeoQuery library to get expression data fro, NCBI GSE. I have succeed to get the ExpressionSet data but notice something strange. It has negative value in it. It is impossible to get the log2 scale with negative value so I'm thinking whether it has been processed beforehand. Does it mean the value is already in log2 scale?

I'm not really familiar with NCBI SOFT or MINIML because I studied how to process microarray data from the raw type data (CEL file). Is it already processed data (log scale or normalization or other data processing method) or just raw data after CEL file is processed. From the boxplot, it seems the data has been processed. This is the link for boxplot image:

https://www.dropbox.com/s/602xf27jaincld2/geo2r.png?dl=0

Thank you for your answer.

Edit by moderator: this question relates to GEO series GSE51791.

I don't know what quantity is being displayed in the boxplots, but it certainly does not look like either expression or log2 expression. The description of the data analysis on GEO is not very unhelpful -- if I had to guess, I would say that they have computed log-intensities in some form, then standardized to have mean 0 and variance 1 for each array.

Anyway, the processed values look suspect to me. Personally, I would re-analyze the data from the raw Feature Extraction files that are provided on GEO as supplementary files. Just go to the GEO page

  http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51791

and click on the link to supplementary files at the bottom of the page.

Dear bharata1803,

It's hard to know for sure since you're not giving us the GSE number.

If I had to guess: M-values, i.e. log2(ch2/ch1), from a two-colour array?

Cheers,

 - axel