User: Lorena Pantano

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Boston
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https://lpantano.githu...
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lopantano
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5 years, 11 months ago
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Posts by Lorena Pantano

<prev • 20 results • page 1 of 2 • next >
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Answer: A: "degPatterns" showed 6 clusters, but why no genes in cluster 1-4, but all cluste
... Hi, Thanks for the question. There is a parameter that is minc, by default = 15 that will remove clusters with less than those genes. Can you try to set up that value to 1 or less and see if you get more clusters. This is an arbitrary value to remove isolated genes and it has to be set up accordi ...
written 6 weeks ago by Lorena Pantano90
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Answer: A: Hill shape p-value histogram after differential miRNA expression analysis with D
... Hi, Although I am not an expert in the use of fdrtool, normally I check I few things to understand the results of differential expression analysis. Just to add some information to your question, How many replicates do you have in each group? Did you plot the new genes are significant to know whet ...
written 3 months ago by Lorena Pantano90
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Answer: A: Whether "read_counts_miRNA" or "reads_per_million_miRNA" to use for DE expressio
... Hi,   I would definitely avoid CPM. In miRNA data normally there are a very few bunch of miRNAs that can be expressed million of times, but this values can vary a lot, and using CPM can lead to increase the real variation of the data. For instance, you can have one sample where 1 miRNA has 1 mill ...
written 11 months ago by Lorena Pantano90
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Comment: C: EdgeR on miRNA data
... Hi, Aaron is completely right about using miRNA if you don't expect total de-regulation. I would say that detect that is pretty complicated, because using everything can introduce a lot of bias, since the library preparation itself could be the cause of different amount of some specific small RNA, ...
written 2.1 years ago by Lorena Pantano90
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Answer: A: miRNA-seq data analysis
... Hi, Normally you do a first analysis for miRNA annotation and so on ourside R, and then use R and bioconductor packages for differential expression or donwstream analysis. It's possible you can do all with R, but we use: https://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html#smallr ...
written 2.2 years ago by Lorena Pantano90
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Answer: A: TPM for miRNA tags
... Hi, I don't think TPM make sense for miRNA in the sense that TPM for mRNA uses the length. I think you can use edgeR/DESeq2 to normalize and you will get a normalized value that can be compared among samples. Do you want TPM for some specific reason? ...
written 2.7 years ago by Lorena Pantano90
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Answer: A: Detect global differences in miRNA expression between tumor and normal using spi
... Hi, You can use any of the methods that people use for mRNA. I use more limma:voom or DESeq2 because in general work better in my case with outliers.  You can check the dispersion figures and MA plot of these packages, and if they look good, you don't need anything special for normalization. If so ...
written 3.9 years ago by Lorena Pantano90
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Comment: C: DESeq2 "DESeqDataSetFromMatrix" function has started to give me an error
... thanks Mike!  didn't have this problem with DESeq2, only having problem with my package: https://github.com/lpantano/isomiRs/blob/develop/R/AllClasses.R. I will ask Herve help because is far from my knowledge. Although the package is not accepted yet. :) ...
written 3.9 years ago by Lorena Pantano90
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Comment: C: DESeq2 "DESeqDataSetFromMatrix" function has started to give me an error
... thanks Mike!  didn't have this problem with DESeq2, only having problem with my package: https://github.com/lpantano/isomiRs/blob/develop/R/AllClasses.R. I will ask Herve help because is far from my knowledge. Although the package is not accepted yet. :) ...
written 3.9 years ago by Lorena Pantano90
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Comment: C: DESeq2 "DESeqDataSetFromMatrix" function has started to give me an error
... it happens to me with a package I am doing when using the develop version of BioC. biocValid() is happy. I was importing SummarizeExperiment from GenomicRanges. Now there is a new package for that class. I am relative new to BioC as developer, so still don't know what is it. Probably with the devel ...
written 3.9 years ago by Lorena Pantano90

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