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Need Control Gene Count Files

I am doing differential expression analysis of isoform quantification data in R studio. I am looking at the floor of mouth, tongue, and tonsil subsites of HNSCC and I am using TCGA for my data. The issue with this is that there is not enough subsite-specific control data. I was wondering if there were any other places where I could get control data that I could just substitute in or if there was more subsite-specific data that I was missing.

r rna-seq tcga
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updated by SHXVRR • SHXVRR • written by Ozymandeus • Ozymandeus

I think very very few people would know that HNSCC stands for Head Neck Squamous Cell Carcinoma in order to understand the context, and therefore what would constitute a control. Is this the data from Sayans et al. 2019 J Clin Med. 8(11): 1896? The problem with swapping in other data sets is that there will be a batch effect confounded with your variable of interest.

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written by seidel seidel

Compare within the dataset. Between subtypes or between samples that express certain markers highly/lowly. You cannot compare between studies quantitatively.

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written by ATpoint ATpoint

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