I'm analyzing some old array data I've inherited and I have a question about filtering the list of genes/probes from which I want to do subsequent analysis, such as generating a heat map or producing a list of deferentially expressed genes. I am comfortable so far in using quantitative metrics to filter out genes (e.g. using TopTable or rowSds).
However, what I'd really like to do is filter out genes according to family or function, i.e. filter out only those genes associated with fatty acid metabolism or cellular metabolism. Or say, cancer related genes. Then from those genes generating a heat map or deferentially expressed genes.
Is there a tool available to do that with Affymetrix arrays? Specifically I am using the HT MG-430 PM array. I've tried searching how to do this but I'm concerned part of the problem for me is that I'm probably using the wrong search terms, so if this is a familiar topic I sincerely apologize. Thank you for your help!
•
written
by
NLP •
1 answer
Note: Typically, one first does the differential expression analysis and then the tests for enrichments of certain categories!
In any case, you will have to map the Affymetrix probes to gene names. Once you have the gene names, you can use myriad packages for functional annotations, e.g. biomartr, Blast2GO, DAVID etc.
That depends a lot on the question. What exactly do you want to achieve? And are you familiar with R or do you prefer a GUI/web-interface?
Log in to answer this question.
-
Remove contamination across cell clusters
written by i.am.filippov •
-
Tutorials on linear models, mixed models, hierarchical models etc. for gene/protein expression
written by The
-
How do I change size of gene names displayed on plotHeatmap from scater R Package
written by gsr9999
-
filtering of genes before unsupervized analysis
written by kanwarjag
-
What is the difference between deferentially expressed genes and deferentially expressed transcrip…
written by WUSCHEL
-
Filter HT-Seq output for gene subclasses
written by rbronste
-
Filter by Fold change in DESeq2
written by EpiExplorer
-
gene names in "Heatmap" function
written by et.kugler •
-
How the level 3 TCGA raw counts are calculated for each sample?
written by pbio
-
Heat Map Of Pan-Genome
written by Robert Jenkins •
