User: baldissera152

baldissera152 • 10

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Posts by baldissera152

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TargetScan target genes are retired, should we use them?

... Hi, guys. I am using [TargetScan Fish][1], which has not been updated in a while, to find targets for a given miRNA. TargetScan Fish provides the gene IDs for representative 3'UTR target genes. I am using bioMart to find the names of these genes and find orthologous in other species. However, when ...

retired gene id ensembl targetscan genome assembly written 11 weeks ago by baldissera152 • 10

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Comment: C: DESeq2 design and Batch effects

... Thank you for your reply. You are right, it's very hard to analyze data when the design is very restrict. The groups I have defined as "acute" and "later" were based on the original paper's findings. My PCA just confirmed a grouping tendency. Regarding my idea of splitting a group based on the PCA ...

written 8 months ago by baldissera152 • 10

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DESeq2 design and Batch effects

... Hi, guys. I am analyzing some RNA-Seq data from animals in different time points after a trauma in the spinal cord. The animal’s tissue have been pooled according to the time-points, therefore I do not have biological neither technical replicates. In order to analyze this data, I have attributed a ...

deseq2 design rna-seq batch effect written 8 months ago by baldissera152 • 10 • updated 8 months ago by ATpoint ♦ 36k

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Differential expression using Scran batch corrected data

... Hi, guys I intend to to integrate two single-cell RNA-Seq datasets and then correct their expression values for batch effect using Scran mnnCorrect function. However, after mnn correction, the output is a matrix which includes logtransformed and negative values. Since softwares usually require raw ...

single-cell batch correction scran rna-seq written 20 months ago by baldissera152 • 10

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