User: Carlo Yague

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Carlo Yague5.2k
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Posts by Carlo Yague

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Comment: C: Suggestion for Differential Expression analysis
... No, this is just a warning, it is not really the issue here. The issue is that you are asking DESeq2 to calculate within group variability (=dispersion) on groups of 1 samples since you have only one replicate by group (=by tissue). DESeq2 obviously can't do that that is why it throws the error `The ...
written 19 days ago by Carlo Yague5.2k
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Comment: C: Why some mapped reads are are not mapped completely?
... Another thing that is also often soft-clipped are adapters. During sequencing, sometimes the insert is smaller than the number of sequencing cycles, so you end up sequencing the insert + a part of the sequencing adapter. This is easy to check in FASTQC, like in the image below. ![enter image descrip ...
written 19 days ago by Carlo Yague5.2k
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Comment: C: Suggestion for Differential Expression analysis
... Can you show the full coldata ? > the same number of samples and coefficients to fit looks like you do not have replicates, which is triggering the error on the design matrix. If you do not have replicates, then you can not use DESeq2 for your analysis. ...
written 19 days ago by Carlo Yague5.2k
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Answer: A: Suggestion for Differential Expression analysis
... Yes, it is an appropriate option to use DESeq2 in your case. Just note that DESeq2 will take into account all the genes to (1) estimate dispersion and (2) normalize your libraries using the median of ratios method. So even if in the end you only look at two genes, all genes are used in the analysis, ...
written 19 days ago by Carlo Yague5.2k
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Comment: C: Correlation in RNAseq
... From the figure, I can tell that they calculated to correlation on **the log** of mRNA abundance, which makes more sense. I haven't read the paper in details but it is unclear to me what they call "mRNA abundance". From what I see, it could very well be read counts per gene. > Besides, I have go ...
written 23 days ago by Carlo Yague5.2k
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Answer: A: Correlation in RNAseq
... Here are a few thoughts: - *"the Pearson correlation coefficient of mRNA abundance"*. I don't think this would be a good idea because mRNA abondance (that is, I guess, read count per gene) follows a long tail distribution that would skew the calculation the correlation. Instead, I would either use ...
written 24 days ago by Carlo Yague5.2k
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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 7 weeks ago by Carlo Yague5.2k
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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 7 weeks ago by Carlo Yague5.2k
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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 7 weeks ago by Carlo Yague5.2k
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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 7 weeks ago by Carlo Yague5.2k

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Teacher 9 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 11 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 3 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 7 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 9 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 11 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 12 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Scholar 12 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 12 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Appreciated 12 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Teacher 12 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 12 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 13 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Commentator 16 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 18 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 18 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 21 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 22 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 22 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 input for DE analysis
Commentator 2.2 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 2.3 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 2.3 years ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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