User: DataFanatic

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DataFanatic300
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Posts by DataFanatic

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Comment: C: Batch correction in DESeq2
... I see. Thank you so much for taking the time to explain this so well!! ...
written 10 weeks ago by DataFanatic300
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Comment: C: Batch correction in DESeq2
... Right, that is step 3 why do I need step 2 in method 1. ...
written 10 weeks ago by DataFanatic300
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Comment: C: Batch correction in DESeq2
... I'm confused about Method 1.step 2. DESeq2 will only take raw counts what kind of normalization can I apply in step 2 that will be compatible with DESeq2? ...
written 10 weeks ago by DataFanatic300
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Comment: C: Batch correction in DESeq2
... Okay, thanks. Is there a need to normalize(B) or just transform the dataset to Z-scores(A)? A) 1. Obtain raw counts 2. Transform to z-score B) 1. Obtain raw counts 2. Normalize( e.g. DESeq2, RPKM, TMP) 3. Transform to z-score Thanks!! ...
written 10 weeks ago by DataFanatic300 • updated 10 weeks ago by Kevin Blighe69k
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Comment: C: Batch correction in DESeq2
... Yes, I have data generated in the lab(heart) and public data(liver). I also have other data that were generated in my lab but in different batches. ...
written 10 weeks ago by DataFanatic300
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Comment: C: Batch correction in DESeq2
... Hi Kevin, You are right what I want to show is actually heat maps of Z-scores comparing expression levels across tissues similar to Figure 4 of Brown et al., 2014. I am still unsure of how I should do this analysis using data generated in two different labs. [https://www.nature.com/articles/natur ...
written 10 weeks ago by DataFanatic300
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Comment: C: Batch correction in DESeq2
... Hi Kevin, Thank you very much. The idea was to use DESeq2 normalization and extract the normalized counts for downstream analysis. To identify tissue-specific genes(lung transcriptome for example), I was planning to do a correlation using the normalized counts. Is there a reference for calculating g ...
written 10 weeks ago by DataFanatic300
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RNA-seq batches across different tissues
... Hi, I have RNA-seq data across different tissues, and I want to identify genes that are uniquely expressed in a tissue of interest. Some of these data were generated in the lab and sequenced in the same lane, and other data comes from public databases. Can I use DESeq2 normalization in this case? I ...
normalization rna-seq written 10 weeks ago by DataFanatic300
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Comment: C: Batch correction in DESeq2
... I have a similar question, I have read many posts on this subject and tried analyzing my data but got an error that I don't fully understand. I would greatly appreciate your help in clarifying what I am doing wrong. I have RNA-seq data across different tissues, and I want to identify genes that are ...
written 10 weeks ago by DataFanatic300
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RAP-seq datasets but no corresponding RNA-seq
... I have a set of TRAP-seq datasets but no corresponding RNA-seq. Can these data be used to report transcription without reporting translation efficiencies? ...
trap-seq translation rna-seq transcription written 10 weeks ago by DataFanatic300

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