User: leaodel

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leaodel80
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2 days ago
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4 years, 9 months ago
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Posts by leaodel

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Problem in hierarchical clustering
... So a batch effect is not something that you'll correct by means of normalization. You have to use a method designed to measure the variance attributed to the batch variable and then correct for it. If you have a hidden batch effect you can use [sva][1]. > The sva package can be used to remove a ...
written 2 days ago by leaodel80
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Answer: A: RNA-seq differential expression : relevance of mixing several datasets
... You should process the data separately and once you have the expression matrix you can use methods like PCA to check if the variability of your data is being driven by the condition of interest. If this is not the case, you have a batch effect on your dataset. If you know what is causing the batch e ...
written 3 days ago by leaodel80
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Answer: A: Problem in hierarchical clustering
... If you have a known batch effect and plan to visualize your data you'll need to correct the log-transformed data for this batch effect. I use limma::removeBatchEffect. ...
written 3 days ago by leaodel80
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... To obtain an expression matrix I normalized raw counts with the median ratio method from DESeq2 and then calculated counts per million with their fpm() function. ...
written 3 days ago by leaodel80
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Answer: A: WGCNA soft thresholding problem
... Hi catagui, I was having the same issue and setting `dataIsExpr = T` on `pickSoftThreshold()` solved things for me. Hope it helps! ...
written 5 months ago by leaodel80
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Answer: A: I meet some problem for using Deseq2.
... Hi, codezy. You should really dive into DESeq2's tutorial, it's an essential resource for learning. With that being said, when you have files from HTSeq you should use another function to import your samples. Try this: Create a variable with the file's path: dir <- "~/pathtoyourfiles/" Add ...
written 6 months ago by leaodel80
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Answer: A: 16S rRNA classification pipeline
... Hi Sus, I would try the [BMP pipeline][1], they provide a detailed pipeline that you can use as it is or construct yours from theirs. You can find a detailed guide for rRNA 16/18 and ITS data analysis. Good luck! [1]: https://www.brmicrobiome.org/target ...
written 6 months ago by leaodel80
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Comment: C: Somatic vs Germline Variant Calling
... I agree with you. I was referring to germline variant call, should've made that clear. My understanding is that you'd need child-parent comparison if you want to find new variants or in a clinical setup. I just have some RNA-seq samples and I want to compare their SNPs. Bottom line, the basic assum ...
written 9 months ago by leaodel80
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Comment: C: Somatic vs Germline Variant Calling
... Thanks, RamRS. I do understand that 'software is dumb' but there must be some underlying assumption to call either somatic or germline variants other than experiment design. Otherwise, we wouldn't need distinct software (I.e., HaplotypeCaller for germline and Mutect2 for somatic, both from GATK). P ...
written 9 months ago by leaodel80
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Comment: C: Somatic vs Germline Variant Calling
... Aside from the conceptual answers on what is somatic and germline, I would very much like to know how a software can tell apart germline and somatic. I know that tools are specific for either somatic or germline variant calling, but other than that what are the basic assumptions that these tools rel ...
written 9 months ago by leaodel80

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Popular Question 4 months ago, created a question with more than 1,000 views. For Best-suited unit of expression to perform between-sample comparison
Student 6 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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