Combining HTSeq and RNA-SeQ for differential analysis
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szomolay • 0
@381a8303
Last seen 7 weeks ago
UK

Hello,

I would like to ask if it is acceptable to do DESeq2 differential expression analysis for comparing disease condition data that was processed using HTSeq and normal condition data that was processed using RNA-SeQC v1.1.9. I do not have the raw count data, only HTSeq for disease and RNA-SeQC for normal. Thank you very much,

Barbara.

RNASeqData • 129 views
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The fact that you don't have raw data indicate that disease and healthy conditions come from different datasets or studies, hence there is most likely a batch effect nested with condition so the analysis is rather flawed anyway. For a more elaborate answer you would need to add some info on the origin and processing of those data.

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The disease data is from TCGA and the normal data is from GTEx. I am trying to do DE analysis and I am aware of the Xena portal where log2(norm_count+1) RSEM data is available for both TCGA and GTEx, but I am unaware of any method that would be widely accepted for DE analysis using normalized RSEM data. Hence, I thought count data may be a better option. Unfortunately, TCGA has HTSeq and GTEX has RNA-SeQC. Thank you vey much for any advice.

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