User: Carlo Yague

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Carlo Yague5.0k
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Posts by Carlo Yague

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Comment: C: edgeR analysis. Is my design matrix correct?
... I agree with ATpoint, your code looks good (as far as I can see) and unless you mixed up sample in the groups, the most likely explanation is that the dispersion estimate is strongly altered by including the whole dataset. It is recommended to include all the data because the dispersion estimate bec ...
written 21 days ago by Carlo Yague5.0k
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Comment: C: FeatureCounts, zero counts from Hisat2 alignment
... Just to make sure, is your reference sequence really the genome ? Or the transcriptome/cDNA ? Having headers like `>itf11g12620.t1` makes it looks like it is a transcriptome sequence, for which renaming the header as `chr13` does not make sense indeed. In addition, if you aligned on the transcri ...
written 21 days ago by Carlo Yague5.0k
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Comment: C: Does PCA results impact on DESeq2 design choices?
... > 1) If you saw such a result, would you interpret it as there is not a > very clear batch effect? All batches (except batch C) fail to include both positive and negative samples. So it is not really possible to distinguish batch effect from virus effect anyway. ...
written 22 days ago by Carlo Yague5.0k
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Comment: C: Benchmarking DESeq / EdgeR / LIMMA vs Lasso vs RF
... To my knowledge, this has never been tested. Dedicated tools to analyze expression data are designed to accommodate specific difficulties, such as the high number of dimension and the usually (very) low number of replicates. I expect regression of any kind to perform poorly in comparison, because o ...
written 22 days ago by Carlo Yague5.0k
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Comment: C: Using rnaseq reference sample across batches
... > if it is advisable for us to resequence treatment "A" group with one > of the samples present in treatment "B" group so that we can use the > new sample from treatment "B" group to normalize the old data from > samples in treatment "B" group. Yes, to perform sound differential express ...
written 25 days ago by Carlo Yague5.0k
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Comment: C: Error: Empty BAM file in DANPOS3
... Hey, this is juste a hypothesis, but coud it be that DANPOS is checking if there are reads assigned to every chromosome listed in the bam header ? When it finds 0 reads for chromosome1, then it gets confused and say that the bam file is empty ? Perhaps you could try to remove the @SQ line for the "e ...
written 7 weeks ago by Carlo Yague5.0k
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Comment: C: RNA-Seq Analysis: To sort or not to Sort?
... Hi, to be honest, I never tried to sort a file that large, but yeah, the larger the file, the longer it takes... In such a case, it becomes especially important to optimize the `-@` and `-m` parameters of samtools (number of threads and available memory per thread). Hope this helps. Carlo. ...
written 7 weeks ago by Carlo Yague5.0k
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Comment: C: DESeq2-Differential expression Number limitation
... There are multiple fix to this, but in your case, the easiest would be to call the count() function after the DESeq() fonction. So `counts(dd, normalized=T)` should work. ...
written 8 weeks ago by Carlo Yague5.0k
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Comment: C: DESeq2-Differential expression Number limitation
... I would not say this is wrong, but perhaps a little bit worrying about the data quality. The study does not see underpowered in terms of replicates (22), but perhaps the read counts are very low ? You can easily check that using a MAplot. Or perhaps there is a huge variability between replicates ? C ...
written 8 weeks ago by Carlo Yague5.0k
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Answer: A: Reliability of gene expression with low exonic counts in bulk RNA-seq data
... > very high % of intronic counts (40-60% of mapped reads), which I > believe come from pre-mRNA fraction This is very unlikely with bulk RNA, unless you are not doing RNA-seq *per se* but some kind of nascent RNA-seq (NET-seq for instance). I think this is more likely to come from genomic DNA ...
written 10 weeks ago by Carlo Yague5.0k

Latest awards to Carlo Yague

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Appreciated 11 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Scholar 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Appreciated 11 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 12 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 17 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 17 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 20 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 input for DE analysis
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 2.2 years ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 2.2 years ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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