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Created by Sara Gosline sgosline Sorry for multiple questions - it looks like that integer featureCount data just has the cNF patient counts, not collated with normal controls from ENCODE. Am I misinterpreting? Yes the count matrices we collated are in syn6101457.
-sara Thank you! Is there a merged integer count matrix file of the control and cNF RNAseq data? I'm having trouble with DESeq2 and figuring out where to get my inputs. This is an excellent question! @allawayr and I have tried to use [ENCODE-derived skin samples](https://www.synapse.org/#!Synapse:syn6035833) as normal control and I have given you access to those on Synapse, but they are not patient specific and suffer from large batch effects. Unfortunately the ethics of the physician collecting samples prevented the collection of additional tissue. Has anyone using the cutaneous Neurofibroma RNA-seq data for analysis found a good source of data to use for normal controls that are a good match for the 11 patients from this data? Thanks!
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