User: bioinfo20014

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bioinfo2001420
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Posts by bioinfo20014

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Comment: C: contrast design of DESeq2 for correlated data
... You are right, I have control and treatment for each replicate and cell line. I have been using ~cell + condition, but I just wanted to make sure I shouldn't be doing something else, so thanks for the clarification. For others reading this thread in the future, this is the design I have: sample ...
written 3 months ago by bioinfo2001420
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Comment: C: contrast design of DESeq2 for correlated data
... Hi, Michael, first of all thanks a lot for helping DESeq2 users! Regarding the correlation between samples from the same individual, do you think that it is always necessary to duplicateCorrelation() and limma? How well do you think DESeq2 performs when there are correlated samples that are not str ...
written 3 months ago by bioinfo2001420
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Comment: C: Differential expression due to extreme outliers in DESeq2
... Thanks for the suggestion, Mike. Now that gene has pvalue = 0.31 and padj = 0.58. Another gene that had the same problem also has higher padj. ...
written 7 months ago by bioinfo2001420
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Comment: C: Differential expression due to extreme outliers in DESeq2
... Sorry, I replied too fast. I do get NA for both pvalue and padj using defaults (cooksCutoff = TRUE and independentFiltering = TRUE). ...
written 7 months ago by bioinfo2001420
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Comment: C: Differential expression due to extreme outliers in DESeq2
... baseMeanA           116.779010545804 baseMeanB           11.5170403274273 baseMean              60.099488120524 log2FoldChange    -3.33358245938423 lfcSE                      0.955682659416467 stat                        -3.48816882522457 pvalue                   0.000486340890441655 padj           ...
written 7 months ago by bioinfo2001420
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Comment: C: Differential expression due to extreme outliers in DESeq2
... When I use cooksCutoff this gene has an NA adjusted P-value. I may be misremembering the post I'm looking for, but I thought there was a way to still include these cases but make DESeq2 somehow consider all replicates individually. In cases like this, the gene is simply excluded from analysis or ca ...
written 7 months ago by bioinfo2001420
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Comment: A: Differential expression due to extreme outliers in DESeq2
... Thanks for your reply, Michael. Here's an example of the case I have in mind. These are TPMs: wt1    53.18 wt2    2.81 wt3    3.58 wt4    3.03 wt5    2.31 wt6    2.69 ko1    1.79 ko2    2.98 ko3    3.54 ko4    3.35 ko5    3.22 ko6    4.07 ko7    2.1 wt1 has an extremely high TPM compared to the ot ...
written 7 months ago by bioinfo2001420
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Differential expression due to extreme outliers in DESeq2
... A couple of weeks or months ago, a question was posted regarding DESeq2's behavior when dealing with samples with one extreme outlier. In that case, DESeq2 identified that gene as DE, although there was only 1 out of N samples with extreme counts. Michael Love suggested a way to force DESeq2 to loo ...
deseq2 outliers written 7 months ago by bioinfo2001420
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Comment: C: How to use RUVSeq in clustering problems?
... Thanks for your reply. I'm actually using the DESeq2 normalized counts, not rlog, unlike I said. I also tried using raw counts and the betweenLaneNormalization function but got similar results. I am going to try what you suggested. ...
written 9 months ago by bioinfo2001420
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How to use RUVSeq in clustering problems?
... I have successfully used RUVSeq to correct samples from a "classical" control vs treatment experiment for batch effects using RUVr, RUVg, RUVs and svaseq and all gave similar results, which were satisfactory. Now I want to use RUVSeq in a clustering problem and I understand I can only use RUVs. I ...
clustering ruvseq rna-seq written 9 months ago by bioinfo2001420 • updated 9 months ago by davide risso740

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