User: January Weiner

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Posts by January Weiner

<prev • 36 results • page 1 of 4 • next >
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Bioconductor package implementing the GOrilla algorithm
... Hello, is there an easy way to use the GOrilla algorithm in R? (http://www.biomedcentral.com/1471-2105/10/48) It allows to find significant enrichment in an ordered list rather than by comparing two groups (DE vs background as most of enrichment analysis algorithms use). Best regards, j. -- ---- ...
written 5.4 years ago by January Weiner360
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Comment: C: Influence of expression correlation on false positive ratio
... Hi Jeff, many thanks. > If the tests are only dependent in small groups, say because genes are > grouped into small modules, then most FDR methods in the p.adjust() > function or the methods in the qvalue package will work. Yes, but I wonder how it behaves in light of a more extensive co ...
written 5.4 years ago by January Weiner360
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Influence of expression correlation on false positive ratio
... Hello, statistical methods for assessing significance of differences in expression assume, correct me if I'm wrong, independence of the tests. Does anyone have at hand any papers on the performance -- in terms of type I error -- of methods such as limma / eBayes? I'm sure this issue has been invest ...
limma written 5.4 years ago by January Weiner360 • updated 5.4 years ago by Jeff Leek490
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Changing results depending on context
... Dear all, I am evaluating a collection of two-color arrays. There are several sets corresponding to different tissues, there is a treatment (common for each tissue), and the treatment effect is analysed independently in each of the tissues. I am analysing the data using limma. The results in terms ...
limma written 5.4 years ago by January Weiner360 • updated 5.4 years ago by James W. MacDonald45k
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Comment: C: Separating channels of a two-color microarray
... Dear Naomi, > After single channel normalization, I usually use MA.RG to transform back to > R and G. ?It has worked remarkably well. Yes, this is also my usual procedure. However, as you noticed, this does not help us with getting rid of the intra-array correlation. I was hoping that there ...
written 5.8 years ago by January Weiner360
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Separating channels of a two-color microarray
... Dear all, first, I would like to thank all who answered my questions in the past. I am attempting a meta-analysis of several microarray studies, with limma as my working horse. I plan to throw all the microarrays together, creating one large data set with one of the factors in the analysis being t ...
microarray written 5.8 years ago by January Weiner360 • updated 5.8 years ago by Naomi Altman6.0k
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Randomisation / resampling and multiple corrections
... Dear all, randomisation or resampling is viewed by some as an alternative to correction for multiple testing such as Bonferroni or Holm. Is there any package implementing such an approach in microarray analysis? Cheers, j. -- -------- Dr. January Weiner 3 -------------------------------------- ...
written 6.3 years ago by January Weiner360 • updated 6.3 years ago by James W. MacDonald45k
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Selecting genes for machine learning
... Dear all, what is currently regarded as the optimal strategy to select genes for machine learning analysis? Taking all of the 40k or so genes is not doable (at least with randomForest, which I use). "Bioconductor case studies" suggests using nsFilter with argument var.cutoff=0.75, however I am not ...
written 6.4 years ago by January Weiner360 • updated 6.4 years ago by Djork Clevert210
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Answer: A: BLAST in R
... Dear Zoha, I think the simplest thing to do is to invoke the command line blast from R, using the option -m 8 to get tabular output that can be automatically parsed by read.table. Example: myPipe <- pipe( "blastall -p blastp -i text.fasta -d data.fasta" ) results <- read.table( myPipe ) coln ...
written 6.5 years ago by January Weiner360
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Testing biased microarray data
... Dear all, the following problem: samples are either RNA, or RNA with selective depletion of some forms of RNA. In short, the relative abundance in the second group of samples should always be equal to or smaller than that in the control, but never higher. The difference in abundance might concern a ...
qpcr limma written 6.7 years ago by January Weiner360 • updated 6.7 years ago by Simon Anders3.4k

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