User: Andy91

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Andy9160
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Netherlands
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6 months, 1 week ago
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Posts by Andy91

<prev • 17 results • page 2 of 2 • next >
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Downloading Twochannel microarray data from ArrayExpress
... Dear Bioconductor, I am currently in the process of performing a study on various microarray datasets, some of which are two channel microarrays. For consistency reasons, I would like to download the raw two channel data. As such I resorted to the “ArrayExpress” R package. I have experienced quite ...
microarray twochannel arrayexpress written 9 months ago by Andy9160
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Meta Analysis on CAMERA results
... Dear all, I would like to perform a meta analysis on the gene sets that I observed using CAMERA. Has anybody had experience with comparing gene sets between studies that performed the same experiment? Would it make sense to extract the t-statistic from CAMERA and use that to calculate the Cohen d a ...
limma camera meta analysis cohen d written 17 months ago by Andy9160
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Answer: A: UcscTrack and BED without headers
... Thanks for the great work! ...
written 2.6 years ago by Andy9160
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Answer: A: UcscTrack and BED without headers
... I see my problem now, I should have paid more attention to the Browser.  If an empty DataTrack could be returned, that would be perfect. Thanks for the answers! ...
written 2.6 years ago by Andy9160
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UcscTrack and BED without headers
... Dear all, I am trying to use Gviz to plot the H3K27Ac mark as retrieved from the UCSC Genome Browser. So I based my code off the Gviz tutorial for DataTrack-like tracks: gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX", track = "Conservat ...
gviz ucsc bed ucsctrack written 2.6 years ago by Andy9160
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Comment: C: Understanding contrasts limma
... Thank you for your answer. I am still trying to wrap my head around this concept. I am still struggling with the idea of why "trt3"  influences the estimated variance of "trt1" with "trt2"? Is this similar to the question described in the link below? https://stat.ethz.ch/pipermail/bioconductor/2012 ...
written 2.9 years ago by Andy9160
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Understanding contrasts limma
... Dear all, I am having some conceptual issues with the contrasts generated by limma. From my understanding, contrasts acts as an method for defining comparisons between groups. For example, we have expression data of six samples with two samples being controls ("trt1"), two samples being treated wit ...
limma design and contrast matrix written 2.9 years ago by Andy9160 • updated 2.9 years ago by Aaron Lun20k

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Popular Question 17 months ago, created a question with more than 1,000 views. For Understanding contrasts limma

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