Possible Data integration of molecular data(transcriptomic) and imaging data from the same patients in R
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svlachavas ▴ 800
Last seen 5 days ago
Germany/Heidelberg/German Cancer Resear…

Dear Bioconductor Community,

i recently acquired a excel file of PET data regarding some variable measurements on colon cancer patients(i.e., SUV, k1, k2) with totally 7 different variables. As i have also performed a microarray data analysis on the same patients to find DE genes between colon cancer and normal samples, i would like to ask if anyone can propose a possible data integration of these molecular and imaging data, in order to extract possible interesting biomarkers or also other aplications. As i have not experience in such methodologies, is there a pipeline for interpretation in r/bioconductor and/or some tutorials ? I searched the literature but i have noticed a very few examples or methodologies regarding molecular and imaging data.

data integration microarray bioconductor affymetrix biomarkers • 1.1k views
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Last seen 8 days ago
EMBL European Molecular Biology Laborat…

As far as I understand your question this is not really specific to imaging - rather, you have 7 phenotypic features which you can correlate with the expression data, or the diagnosis, with the usual methods (regression, classification, hypothesis testing, canonical correspondence analysis).

As for taking image data and extracting quantitative features, there are many approaches and options; the EBImage might provide some useful tools.

Hope this helps



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Dear Wolfgang,

thank you for your notifications and considerations on this matter. Thus, as i have not prior experience in classification or regression analysis, should i search for the above methods you proposed and use the above PET metrics as "phenotypic features-variables" in order to extract possible correlation with expression data ?


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