venn diagram of rna seq and microarray datasets
I am working on Chister platform. When i work on microarray and make two group testing statistics, the resulting tsv file does not include the genes by Ensemble identifier, but numbers_at. when i use venn diagram to find the common DEGs with tsv file from rna seq analysis, and tsv file from microarray analysis this give zero genes in common. Please tell me how to get DEGs .tsv files from microarray analysis containing Ensemble Identifier to get common DEGs with rna seq datasets.
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M.Mohareb •
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Before comparing the lists convert the array ids to the ensemble gene ids. Check the attached thread to know how to convert microarray ids. Converting Affymetrix Probes To Gene Ids
If you have a list of genes, you can also do it online. Have a look at https://www.ebi.ac.uk/training-beta/online/courses/array-express-discover-functional-genomics-data-quickly-and-easily/next-steps-towards-data-analysis/opening-and-processing-raw-data-files/microarray-experiments/tools-for-conversion-of-probe-ids/
Hello dear, Many thanks for your kind reply. I need to know about the fc, p value and adjusted p value of each gene in the tsv file that can be created by finding the common DEGs between 2 or 3 datasets using venn diagram. Which p value or fc value is chosen by venn diagram for a certain DEG that is commom between more than 2 dataset. for example, if i have a DEG that is differentially expressed in dataset 1 with adjusted p value of 0.03, and daraset 2 with adjusted p value of 0.01, what will be the adjusted p value in the tsv gile containing the common DEGs. Thanks.