User: mismis

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mismis0
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Posts by mismis

<prev • 4 results • page 1 of 1 • next >
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Comment: C: Microarray outlier - how to deal? Downweigh? Remove? Re-run everything?
... Hi, I tried to follow up with your suggestions - the results are below: QC including PCA plot, boxplots, heatmap, MA-plots (all pre-normalisation): [QC report][1] [dendrogram - euclidian distance, complete linkage][2] [dendrogram - euclidian distance, single linkage][3] [dendrogram - euclidian d ...
written 2.0 years ago by mismis0
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Comment: C: Microarray outlier - how to deal? Downweigh? Remove? Re-run everything?
... The QC generated with arrayQualityMetrics for the summarized set before normalization is here, including PCA plot and boxplots (non-normalized, looks ok as well after normalization): [QC report][1] As for the different dendrograms - I'll check tomorrow! @Kevin Blighe: Thank you very much for your ...
written 2.0 years ago by mismis0
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Microarray outlier - how to deal? Downweigh? Remove? Re-run everything?
... Hello dear community, we recently submitted an experiment with multiple celllines, control vs. treatment, 3 biological replicates per condition per cellline for expression profiling using Illumina HT-12 microarrays. In the original run, we tried to counter batch effects by blocking and randomizati ...
illumina-ht12 outlier qc microarray limma written 2.0 years ago by mismis0 • updated 2.0 years ago by Kevin Blighe51k
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Help w. workstation specs for human exome-seq/variant calling and microarrays? Cores vs speed, RAM
... Hello, we are currently planning a project that is going to involve exon sequencing as well as microarrays for expression and methylation analysis and I am looking for advice for the hardware side of things. Even if final analysis would run e.g. on external servers, we still need a workstation for ...
microarrays hardware exon-seq written 2.8 years ago by mismis0

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