User: stevenmarkgalway

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Posts by stevenmarkgalway

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Comment: C: Analysis Without Replicates
... OK something that I am trying to get my head around. Given this scenario: I have a read count for GeneA for both control and case samples (no replicates). Gene A(control) has a read count =2, GeneA(case) has a read count=1000. That is approximately a 9 fold increase for GeneA(case) at the log2scale ...
written 2 days ago by stevenmarkgalway10
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Comment: C: Analysis Without Replicates
... It seems I can't run the LFC shrinkage without first running the DESeq function, which in-turn requires replicates - "Treating samples as replicates was deprecated in v1.20" ~ output from DESeq2. So I will stick with the regularised log fold change. I was considering a high read count cutoff, but I ...
written 2 days ago by stevenmarkgalway10
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Comment: C: Analysis Without Replicates
... That's exactly right Kevin, it's the Log2(1.5). After reading around I gathered some ideas for what I might be able to do in this situation. I guess being new to this kind of analysis there is a degree of uncertainty on my behalf. I just wanted to see what people thought. Thanks a lot for your input ...
written 3 days ago by stevenmarkgalway10
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Comment: C: Analysis Without Replicates
... Thanks for your feedback guys, much appreciated. Yeah, I have absolutely no replicates and yes they have been processed in the same batch. I did try duplicating the data for DESeq2 analysis, but no joy. I think going of estimated p-values for experiment without replicates is prob not a great idea an ...
written 3 days ago by stevenmarkgalway10
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Analysis Without Replicates
... I am carrying out an RNA-seq analysis on mesenchymal stem cells retrieved from disease and control state. However, the exp is without replicates (bad idea I know). The analysis is exploratory, to identify potential factors that can be validated in the lab. So far, I performed transcript quantificati ...
replicates without rna-seq written 3 days ago by stevenmarkgalway10

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