User: Martombo

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Martombo2.4k
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Posts by Martombo

<prev • 296 results • page 1 of 30 • next >
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Comment: C: Deseq2 positive results for genes highly variable between replicates
... In my experience, this kind of result typically stems from the presence of a very high variability in samples of the same group (compared to between groups). You may want to correct for possible co-variates in your data (see svaseq) or simply filter out results with high dispersion. ...
written 1 day ago by Martombo2.4k
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Comment: C: Error in some hog codes using pyham
... this is the best name for a package in the history of bioinformatics! ...
written 3 days ago by Martombo2.4k
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Comment: C: Removing adaptors from smallRNA seq data
... well it does seem like 60% of reads were trimmed, right? ...
written 4 days ago by Martombo2.4k
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Comment: C: Removing adaptors from smallRNA seq data
... Do a multiple sequence alignment of the last ~15 nucleotides of some hundred of reads and you should be able to identify the sequence of your adapter ...
written 5 days ago by Martombo2.4k
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Comment: C: Selecting the consensus/overlapped genes from the DE study
... As they state in the paper you linked, it is expected that by taking the overlap of different tools you improve the absolute accuracy measures. As I mentioned in my original comment, you will select genes whose differential expression is simply more significant. You can however also do that by lower ...
written 12 days ago by Martombo2.4k
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Comment: C: Finding the best combination of covarites in a multivariate linear regression
... Are the numbers of genes / patients you mention as examples the ones you are actually working with? It is a bit hard to understand from your question. In that case, I would use some machine learning to select features if needed (lasso) and model the explanatory variable of OS (random tree). ...
written 25 days ago by Martombo2.4k
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Comment: C: how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
... I think you can definitely use ESTIMATE with RNA-seq data as this was done by the authors themselves. See the tool's [website][1]. [1]: https://bioinformatics.mdanderson.org/estimate/index.html ...
written 4 weeks ago by Martombo2.4k
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Comment: C: Question about differentially expressed genes selection for low sample size data
... I think you can talk about a "trend" in this case, but additional validation is needed. ...
written 6 weeks ago by Martombo2.4k
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Comment: C: Differential analysis using cell-line data with replicate information
... How does a PCA plot of the whole dataset look like? If your cell lines are considerably different (which is very likely), you are better off performing a separate analysis for each cell line. ...
written 6 weeks ago by Martombo2.4k
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Answer: A: Co-expression analysis for genes coexpressed with gene X, genes X and Y, etc.
... I guess you could start by checking which (if any) of your genes of interest are significantly coexpressed. In that way you could use pairs / groups of genes to define a profile of expression. After that, you can determine which other genes are most coexpressed with these modules, or each of your ge ...
written 6 weeks ago by Martombo2.4k

Latest awards to Martombo

Epic Question 4 months ago, created a question with more than 10,000 views. For Sjdboverhang Option In Star
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Student 7 months ago, asked a question with at least 3 up-votes. For Sjdboverhang Option In Star
Popular Question 7 months ago, created a question with more than 1,000 views. For human Natural Antisense Transcript database
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 16 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 16 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 17 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Popular Question 18 months ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Scholar 18 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Appreciated 23 months ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: RNA-Seq counts for all genes?
Great Question 2.1 years ago, created a question with more than 5,000 views. For Sjdboverhang Option In Star
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Tophat --max-multihits option
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Popular Question 2.8 years ago, created a question with more than 1,000 views. For different output format in Clustal-Omega
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction

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