User: jaro.slamecka

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jaro.slamecka100
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Mitchell Cancer Institute, Mobile AL, USA
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Posts by jaro.slamecka

<prev • 18 results • page 1 of 2 • next >
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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 3 months ago by jaro.slamecka100
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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 3 months ago by jaro.slamecka100
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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 3 months ago by jaro.slamecka100
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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 4 months ago by jaro.slamecka100
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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 4 months ago by jaro.slamecka100
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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 4 months ago by jaro.slamecka100
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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 4 months ago by jaro.slamecka100
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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 4 months ago by jaro.slamecka100
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Comment: C: Removing batch effects from microarray data based on only a subset of samples
... Here is a PCA plot and a boxplot without the batch correction and before normalization: Even though the PCA plot looks fine after the batch correction, my issue is that hierarchical clustering shows the replicates of the control samples (LINE1, 2 and 3) not clustering together which reflects on t ...
written 4 months ago by jaro.slamecka100
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Removing batch effects from microarray data based on only a subset of samples
... I am wondering if there is a way to remove batch effects from microarray data based on only a subset of samples. The thing is that the controls in the data are homogenous and the experimental samples are much more heterogenous, as seen from the PCA plot (created after removing batch effect with ComB ...
microarray limma combat removebatcheffect() written 4 months ago by jaro.slamecka100

Latest awards to jaro.slamecka

Popular Question 12 months ago, created a question with more than 1,000 views. For Problem with reading raw Illumina Human HT-12 v4 data using beadarray
Scholar 12 months ago, created an answer that has been accepted. For A: Gene expression differential analysis using TCGA dataset
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Microarray analysis of .adat files to identify degs
Scholar 3.2 years ago, created an answer that has been accepted. For A: Gene expression differential analysis using TCGA dataset

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