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scRNA gene expression without control/comparator

Hi everyone,

I recently had a patient with a very rare lymphoma type and was able to perform scRNA-Seq of a fresh lymph node biopsy. Is there a way to check for differential gene expression based on one single sample, as I do not have any further (non-lymphoma) material from this patient to compare with his lymphoma sample?

I am grateful for any input!

Thanks a lot & best wishes

rna-seq
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updated by jared.andrews07 jared.andrews07 • written by yakumo • yakumo

1 answer

Sure, you can compare between clusters. But in terms of "malignant vs non-malignant" type comparisons, that depends on whether you can separate those populations with any confidence. If malignant tissues/cells have known markers, you can try to use those to classify cells/clusters as malignant or non-malignant cells. Immune profiling is useful for this in many lymphomas as well, which is something to keep in mind for future experiments.

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written by jared.andrews07 jared.andrews07

Thanks for your reply! Can you by any chance recommend a tool/package for this type of analysis? With DESeq2 I find it rather difficult, as it seems to require two sets of values to compare in order to perform differential analysis (at least that's the error message I receive when I try to run it on a single column of gene expression counts)... Many thanks!

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written by yakumo • yakumo

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