User: jaro.slamecka

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Location:
Mitchell Cancer Institute, Mobile AL, USA
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2 days, 10 hours ago
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Posts by jaro.slamecka

<prev • 8 results • page 1 of 1 • next >
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Answer: A: How to make a (limma) heatmap displaying gene ID's as rownames
... As Aaron suggested, this is done by specifying the labRow argument, try adding labRow=fData(eset)[["SYMBOL"]] to your list of arguments for heatmap.2: heatmap.2(y[rownames(tab1),], main="Leptin-A Morphant", ylab="Probeset ID",     xlab="Microarray Sample",col=greenred(75),cexRow=0.5,scale="none",ke ...
written 14 months ago by jaro.slamecka30 • updated 14 months ago by Gordon Smyth32k
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(Closed) package lumi is not available (for R version 3.3.2)
... Hi, anyone have an idea about why this error message appears? > biocLite("lumi") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31). Installing package(s) ‘lumi’ Warning message: package ‘lumi’ is not available (for R version 3.3.2) This h ...
lumi illumina human ht-12 v4 written 14 months ago by jaro.slamecka30 • updated 14 months ago by James W. MacDonald45k
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Unexpected clustering of samples after batch effect removal with ComBat
... Hi, I'm trying to find differentially expressed genes between two expression microarray datasets, both Illumina HT-12 v4, one only has 3 samples (3 different patients), the other one has 5 in triplicates (biological, clones). I loaded the datasets using lumi and individually transformed them (vst) ...
combat written 2.8 years ago by jaro.slamecka30
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Answer: A: Gene expression differential analysis using TCGA dataset
... "My problem is, how can I create the phenotypic data to integrate with my expression data?" I'm new to microarray data analysis but to address this particular issue I've created the data frame containing phenotype data in Excel. See the attached screenshot. The number of rows has to match the n ...
written 2.8 years ago by jaro.slamecka30
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Comment: C: Question about the proper way to combine Illumina Human HT-12 v4 expression data
... Yes it would, the dataset1 has 3 samples and the dataset2 has several groups of 3 samples so the differential expression analysis would be done between the dataset1 and the individual groups from dataset2. ...
written 2.8 years ago by jaro.slamecka30
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Question about the proper way to combine Illumina Human HT-12 v4 expression datasets from different labs
... Hi, I tried to study as much as I could about the matter but I'm still confused. I have an Illumina Human HT-12 v4 expression data from our lab's RNA samples. I would like to see if I can combine the dataset with one I downloaded from GEO, also an HT-12 v4, to see differentially expressed genes betw ...
combat batch effect written 2.8 years ago by jaro.slamecka30
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Answer: A: Problem with reading raw Illumina Human HT-12 v4 data using beadarray
... Thank you both so much for your help! Too bad the core lab didn't set the iScan to include the XY coordinate data, I'll make sure they do the next time. And I will look into read.idat in limma. Jaro ...
written 2.9 years ago by jaro.slamecka30
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Problem with reading raw Illumina Human HT-12 v4 data using beadarray
... Hi, I am new to microarray data analysis, trying to put the pieces of puzzle together. Trying to read raw Illumina Human HT-12 v4 data using beadarray. My raw data folder contains csv, txt, EIF, idat, locs, tif, xml file for each of the 12 samples. There is one sdf file, one metrics.txt file and 3 ...
beadarray readillumina written 2.9 years ago by jaro.slamecka30

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Scholar 2.8 years ago, created an answer that has been accepted. For A: Gene expression differential analysis using TCGA dataset

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