User: jaro.slamecka

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jaro.slamecka130
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Mitchell Cancer Institute, Mobile AL, USA
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Posts by jaro.slamecka

<prev • 20 results • page 1 of 2 • next >
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Comment: C: extracting gene names, gene id and transcript id
... It needs to be either Ensembl or UCSC (you'd use it with gtf=ucscGenome()), that's the limitation. What exactly is the GTF file from the STAR website you describe? Can you post a link to it? ...
written 4 months ago by jaro.slamecka130
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Answer: A: extracting gene names, gene id and transcript id
... If you can use an Ensembl GTF, one easy and fast way is to use the refGenome package library(refGenome) gtf = ensemblGenome() read.gtf(gtf, filename="Homo_sapiens.GRCh38.93.gtf") genes = gtf@ev$gtf[ ,c("gene_name","gene_id","transcript_id")] ...
written 4 months ago by jaro.slamecka130
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Comment: C: Tissue Specificity R-package
... I'd say the main advantage is that the authors curated lots of datasets derived by expression profiling of real tissues. So as a biologist if you're developing a new protocol to engineer cells and tissues (e.g. by differentiation of pluripotent stem cells), it can help you check how well you've done ...
written 11 months ago by jaro.slamecka130
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Answer: A: Tissue Specificity R-package
... Take a look at CellNet from Dr. Patrick Cahan's lab, it uses gene regulatory networks to classify samples into around 14-16 tissue types. It works with human and mouse bulk and single-cell RNA-seq data but it also includes tools for training new tissue types. CellNet classifies and scores the simila ...
written 11 months ago by jaro.slamecka130
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Answer: A: How do you re-order .fcs files in a flowSet?
... This can be done by subsetting the flowSet with the re-ordered sample indices, e.g.: set2 = set1[c(5,7,1:3,4,8)] then check the order of the samples sampleNames(set2) ...
written 11 months ago by jaro.slamecka130
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Comment: C: Microarray analysis of .idat files to identify degs
... It looks okay, just not sure why you're taking the genes from datanorm using the argument genelist, instead of letting topTable do the default of taking it from fit2. Given the default behavior of topTable and the fact that you only have one contrast, all you'd need is: output = topTable(fit2, numbe ...
written 11 months ago by jaro.slamecka130
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Comment: C: Microarray analysis of .idat files to identify degs
... You're almost there, assuming you know which samples belong to which group, just manually create the factor f. You have 20 IDAT files so the length of the factor f will also have to be 20 with at least 2 levels, you can simply do something like this, depending on the order of your samples in the dat ...
written 11 months ago by jaro.slamecka130
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Answer: A: Microarray analysis of .adat files to identify degs
... You can try using the function read.idat in limma directly to read the IDAT files into R and create an EListRaw object. You'll also need a manifest BGX file that you can download here: https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/humanht-12/HumanHT-12_V ...
written 11 months ago by jaro.slamecka130
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Comment: C: Removing batch effects from microarray data based on only a subset of samples
... Thank you! I'll try your approach ...
written 11 months ago by jaro.slamecka130
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Comment: C: Removing batch effects from microarray data based on only a subset of samples
... Yes, exactly, ideally I'd like to see Control Line1, 2 and 3 cluster together with their replicates since their gene expression pattern should be relatively stable which I have seen in other experiments. They are cell lines derived from 3 different patients with unrelated genetic background. So I wa ...
written 11 months ago by jaro.slamecka130

Latest awards to jaro.slamecka

Popular Question 3 months ago, created a question with more than 1,000 views. For Problem with reading raw Illumina Human HT-12 v4 data using beadarray
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Microarray analysis of .adat files to identify degs
Scholar 6 months ago, created an answer that has been accepted. For A: Gene expression differential analysis using TCGA dataset
Popular Question 19 months ago, created a question with more than 1,000 views. For Problem with reading raw Illumina Human HT-12 v4 data using beadarray
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Microarray analysis of .adat files to identify degs
Scholar 19 months ago, created an answer that has been accepted. For A: Gene expression differential analysis using TCGA dataset
Scholar 3.8 years ago, created an answer that has been accepted. For A: Gene expression differential analysis using TCGA dataset

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