User: Calin-Jageman, Robert

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Posts by Calin-Jageman, Robert

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Comment: C: Comparing across sets of regulated genes -- Strategies?
... Thanks!  I didn't know about the genas function in limma.  It seems like a very good way to get an overall view of similarity between different sets of regulated transcripts. I'm still working through a number of different approaches, and I'll hopefully post a more data-driven list of pros and cons ...
written 9 months ago by Calin-Jageman, Robert30
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Comment: C: Comparing across sets of regulated genes -- Strategies?
... Sorry this wasn't clear.  Each experiment compares tissue from a set of trained animals to matched untrained tissue.  So, by regulated, I mean there is a LFC from trained/untrained that is both statistically and practically significant.  I think this is just a specific case of an issue that often c ...
written 9 months ago by Calin-Jageman, Robert30
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Comparing across sets of regulated genes -- Strategies?
... I'm looking for some comments on different strategies to compare different sets of regulated genes.  I've seen different approaches, and would like to get some insight into pros/cons of each. In my specific application, I have a microarray analysis of gene expression 1 hour after learning, and then ...
limma differential expression written 9 months ago by Calin-Jageman, Robert30 • updated 9 months ago by Lluís R300
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Comment: C: Limma - Two-color group differences *and* correlation with individual difference
... Thanks so much.  limma is incredible, and you are extremely generous to answer so many questions. I tried out the approach you suggested and it seems to work like a charm.  I haven't done this study yet, so I tested using data from a previous study and set the mscores to be the exact LFCs for one t ...
written 9 months ago by Calin-Jageman, Robert30
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Comment: C: First time use of limma for two-color agilent array analysis
... Through painful experience I found that the script I quoted is NOT correct (in most cases).  Specifically, fit <- lmFit(MA2.avg) should have been: design <- modelMatrix(targets, ref="Control") fit <- lmFit(MA2.avg, design) What's tricky about this bug is that lmFit doesn't complain abo ...
written 9 months ago by Calin-Jageman, Robert30
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Limma - Two-color group differences *and* correlation with individual differences.
... I'm using limma in BioConductor to make a simple paired comparison in gene expression.  Now I'd like to run an auxiliary analysis to see if there are individual differences which correlate with changes in gene expression.  I'm having difficulty understanding how to fold this additional research ques ...
regression limma written 9 months ago by Calin-Jageman, Robert30 • updated 9 months ago by Gordon Smyth32k
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Are the logFC confidence intervals returned by topTable adjusted for multiple comparisons?
... I'm using limma to analyze both microarray and qPCR data. For logFC values, I'd like to report CIs. I found that this feature was added to topTable around 2011 (https://stat.ethz.ch/pipermail/bioconductor/2011-January/037579.html) I'm wondering, though: are the CIs produced by topTable expanded for ...
microarray qpcr limma written 3.3 years ago by Calin-Jageman, Robert30 • updated 3.1 years ago by Gordon Smyth32k
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First time use of limma for two-color agilent array analysis
... I've been working on a two-color analysis of a custom-printed agilent array. I'm examining gene expression in CNS samples from Aplysia californica that have undergone unilateral sensitization training. I've got 8 animals, each with a sample from the trained and untrained side of the CNS. Each pair ...
qpcr limma genespring written 3.7 years ago by Calin-Jageman, Robert30 • updated 3.7 years ago by James W. MacDonald45k

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