User: leaodel

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leaodel130
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Posts by leaodel

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Error in strwidth("W", cex = tl.cex) : plot.new has not been called yet
... We have guidelines for posting enough info so people can effectively help you, I suggest editing the post with more info. Also, be mindful that the purpose of this forum is to help with bioinfo questions and not programming. But it looks like you're trying to use a variable that was not defined prev ...
written 7 months ago by leaodel130
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Answer: A: limma::removeBatchEffect and using DESeq2 for RNA-seq differential expression
... You should 1)read the hundreds of posts about this and 2) dive into the docs to have a more thorough explanation, but yes: modeling a batch variable within the design is enough (and I must say more efficient than correcting) to have your batch effect unaccounted for in DE results. For visualization ...
written 7 months ago by leaodel130
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Comment: C: Why I have too many reads non uniquely aligned?
... Additionally, the overlap resolution mode from htseq can influence your final read count stats, chech the [docs][1] to see which mode better fits your data. [1]: https://htseq.readthedocs.io/en/release_0.11.1/count.html ...
written 12 months ago by leaodel130
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Comment: C: How I deal with different lanes in RNA-seq alignment
... It won't! I have processed several datasets where one sample comes with multiple .fastq files due to sequencing depth. It's essentially the same as concatenate - I, of course, tested before using. It's important not to put spaces between the files when you're feeding --readFilesIn. ...
written 12 months ago by leaodel130
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Answer: A: How to convert NCBI gi or protein accession number to GO term?
... Your question is lacking a good structure and example, so people will be limited on how much they can help you. With that being said, if you're simpling looking for GO terms associated with a given gene - without performing functional enrichment analysis - you can use [biomart][1]. Hope it helps! ...
written 12 months ago by leaodel130
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Comment: C: Comparing RNA-Seq data to online databases
... So ATpoint, I was thinking about using a similar approach as you described in your example. Doing a quick test I figured that the batch effect is so huge, that not even correcting by Study was enough. Do you see the same in your analysis or maybe my toy example wasn't effective at all? In the end, i ...
written 12 months ago by leaodel130
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Answer: A: How I deal with different lanes in RNA-seq alignment
... You don't *have* to concatenate your files beforehand when using STAR. Adding the files of read1 (followed by read 2 if using paired end data) separated by comma should do the trick and save you time: `STAR --readFilesIn file1_1.fastq,file2_1.fastq file1_2.fastq,file2_2.fastq` ...
written 12 months ago by leaodel130
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Answer: A: DESeq2 nested effect with 5 variables
... Hi Sandeep. You have 3 identical variables in your design - tissue, temp and time - you won't be able to distinguish the contribution each variable, either in an 'isolated' or in a nested design, in the differential gene expression test. Even if you use one of these variables, you won't be able to i ...
written 14 months ago by leaodel130
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Comment: C: Problem in hierarchical clustering
... Calangoa, if the answer was helpful to solve your problem, please accept it as an answer. ...
written 14 months ago by leaodel130
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... Nop, the function is called fpm which stands for fragments per million. If you have counts and use this function you'll end up with cpm. ...
written 14 months ago by leaodel130

Latest awards to leaodel

Scholar 12 months ago, created an answer that has been accepted. For A: How I deal with different lanes in RNA-seq alignment
Supporter 14 months ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For Best-suited unit of expression to perform between-sample comparison
Student 20 months ago, asked a question with at least 3 up-votes. For Best-suited unit of expression to perform between-sample comparison

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