Category: Quantseq

Exclude pseudogenes and lncRNA’s from DE-analysis?

Hi all, Let’s start off to thank the ones that helped me lately. I almost feel bad for how many questions I have asked in the last weeks, but the answers were always of great help, so thanks for that! And yet I have another question. As described in my…

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RQN value for Quantseq experiment

RQN value for Quantseq experiment 0 Hi guys, I read some conflicting results about the minimum RQN value in Quantseq experiments. What minimal RQN value is acceptable for a human Quantseq experiment? Moreover, is it possible if the majority of the samples have a RQN value > 7, and some…

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Correcting for leukocyt count in QuantSeq analysis

Correcting for leukocyt count in QuantSeq analysis 0 I am conducting a human white blood cell (WBC) QuantSeq analysis. I have heard some stories about the need to correct for WBC count as this could influence the results. I haven’t been able to find literature about this, so my question…

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Use Spike-Ins or TMM-normalization

Use Spike-Ins or TMM-normalization 1 Hi all, Sorry for all my questions lately, but as a novice which has to figure out how to analyse QuantSeq data, this forum has been a great and indispensible help for me. I’m doing a human transcriptomics analysis where we have QuantSeq data for…

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MD plot for every sample (?!)

MD plot for every sample (?!) 0 Dear all, I am conducting a QuantSeq analysis and in the manuals I find online one of the steps include making an MD-plot for every sample. This is considered data exploration as well as a quality control check, this of course sounds very…

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My bioinformatics story

My bioinformatics story 1 Hi all! I am new to the bioinformatics world and due to circumstances I have been given the complete responsibility to perform a human transciptomics data-analysis without bioinformatic background and for now also without supervision. This whole project feels like a big challenge, finding a puzzle…

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Filtering lowly expressed genes

Hello all, I have a quick RNAseq (Quantseq) question for you all! I am analyzing the Quantseq data for 500 patients and am finding my way through the bioinformatic forest. Currently I am working on a way to filter out lowly expressed genes, and I am using the Bioconductor package…

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