Moderator: Carlo Yague

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Carlo Yague5.5k
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Posts by Carlo Yague

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Answer: A: How correlate between transcriptome data and expression, without proteome data?
... > transcription of those proteins I suppose you mean translation ? Transcriptome data (roughly, the results of transcription and degradation on RNA abundance) only reflect the first steps of protein coding gene expression. Yet, it is widely used to assess the impact of mutation or genetic pert ...
written 6 days ago by Carlo Yague5.5k
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Comment: C: During RNA-seq analysis a lot of pseudogenes come up as DE
... > So what does this overexpression of pseudogenes mean? Is it a > technical artifact or could mean something biologically relevant? Any > help/advice is highly appreciated! Have you looked at the genomic location of the pseudogenes affected ? I think that many of them are located in the pe ...
written 7 days ago by Carlo Yague5.5k
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Comment: C: champ.norm task 1 failed - "could not find function "blc""
... > Can you tell me what are the dependencies of RPMM packages? ENmix, MEAT, MethylMix > I don't have the authoritation to install packages. Can you contact an administrator to help you with the issue ? Because if you can't install anything, not even a R package, then there is not much you ca ...
written 13 days ago by Carlo Yague5.5k
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Comment: C: champ.norm task 1 failed - "could not find function "blc""
... Thank you. In the future, if you feel that there is some value in cross-posting (some of us are not in both forums after all), you can do it, but make sure to add a disclaimer in your post with a direct link to the other site. That way we do not duplicate efforts to provide answers. ...
written 13 days ago by Carlo Yague5.5k
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Answer: C: champ.norm task 1 failed - "could not find function "blc""
... Have you tried re-installing the RPMM and ChAMP packages ? if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("ChAMP") install.packages("RPMM", dependencies=T) ...
written 13 days ago by Carlo Yague5.5k
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Comment: C: champ.norm task 1 failed - "could not find function "blc""
... Hello kun8638! It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/p133866/ This is typically not recommended as it runs the risk of annoying people in both communities. ...
written 13 days ago by Carlo Yague5.5k
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Comment: C: champ.norm task 1 failed - "could not find function "blc""
... Hello kun8638, Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. Thank you! ...
written 13 days ago by Carlo Yague5.5k
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Comment: C: editing gtf file
... > what is the easiest way to do this? There are many different ways to parse and reformat text files. The easiest for you will depend on the scripting language you are most familiar with. For instance, I would personally use R (with the `read.table()`, `sapply()` and `strsplit()` functions), but ...
written 13 days ago by Carlo Yague5.5k
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Comment: C: Despite being in 2021
... Hi, Biostar is indexed by google, so that every question and answers have the potential to become useful to others through as simple google search. It is therefore essential to keep the meta-data of a question (title and tags) as clear and precise as possible. Please edit your current title, as it d ...
written 14 days ago by Carlo Yague5.5k
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Comment: C: Will quantile normalization affect the result of the Tau statistic?
... Is it the same Tau as in Kendall's tau correlation coefficient ? If it is so, my understanding is that *Kendall's Tau* is calculated based on ranks, which are preserved after quantile normalization. So it should lead to identical results to calculate Tau before or after quantile normalization. ...
written 15 days ago by Carlo Yague5.5k

Latest awards to Carlo Yague

Scholar 6 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 12 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Appreciated 25 days ago, created a post with more than 5 votes. For A: RNA-SEQ: Lowering fold change cutoff from 2 to 1.5.
Scholar 5 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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
Scholar 6 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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
Teacher 3 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 4 months 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 4 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
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
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
Commentator 13 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 13 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Scholar 13 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 14 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Appreciated 14 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Teacher 14 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 14 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 15 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Commentator 18 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 19 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 20 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 22 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value

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