User: Guiyuan Lei

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Guiyuan Lei90
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Posts by Guiyuan Lei

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Answer: A: How to set "Pearson correlation " as similarity measure in qtclust() for doing Q
... Hi again, I think I know how to set those parameters by constructing "kccaFamily" object now. mycont=list(iter.max=1000,ntry=nrow(ClusterData),min.size=10) as(mycont,"flexclustControl") mykccaFamily<-kccaFamily(dist=distCor,similarity=TRUE) #minimum correlation 0.9 c11<-qtclust(ClusterData,f ...
written 11.2 years ago by Guiyuan Lei90
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How to set "Pearson correlation " as similarity measure in qtclust() for doing QT cluster
... Dear all, I try to use qtclust() (package flexclust) to do QT (quality threshold) clustering. But I don't know how to set "Pearson correlation " as similarity measure. I would like to know how to set "Minimum correlation" ( for example 0.9) as well. Anyone has any idea? Or is there any other packa ...
written 11.2 years ago by Guiyuan Lei90
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Comment: C: Why NONE of any contrast is significant when overall F-test is significant? usin
... Thank you, Jim. I also tried "separate" and "nestedF". For "separate" method, there are also genes (around 8% of 397 significantly differential genes by F-test) got five '0's. As for "nestedF", every gene got at least one non-zero value. In the post https://stat.ethz.ch/pipermail/bioconductor/20 ...
written 11.6 years ago by Guiyuan Lei90
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Why NONE of any contrast is significant when overall F-test is significant? using "global" method in decideTests() from limma package
... Dear all, I am using limma package to identify differential expression. I have 5 contrasts, I used F-statistic to measure significant differential expression, the F-test p-value is adjusted by "fdr" method . I used the command p.adjust(eb$F.p.value, method="fdr") < 0.05 where eb is the objec ...
limma written 11.6 years ago by Guiyuan Lei90 • updated 11.6 years ago by James W. MacDonald51k
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Comment: C: Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
... Hi, Thank Marc to point out the possibility that Bioconductor annotations to have more information about a particular field (like a gene symbol) than Affymetrix. As for the mask file, the Affymetrix support said that "Only the csv annotation file is updated whereas the mask files are not. Theref ...
written 11.9 years ago by Guiyuan Lei90
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Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
... Hi Jim, Thanks for suggestion. In order to get the gene names/symbols for cerevisiae probesets as much as possible, I donwloaded Yeast2 annotation from Affymetrix http://www.affymetrix.com/Auth/analysis/downloads/na24/ivt/Yeast_2.na2 4.annot.csv.zip Firstly, I found that Bioconductor have got more ...
annotation yeast2 biomart written 11.9 years ago by Guiyuan Lei90 • updated 11.9 years ago by Marc Carlson7.2k
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Comment: C: Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
... Hi Jim, Many thanks. I have checked the s_pombe.msk and s_cerevisiae.msk files, the overlap between pombe and cerevisiae are probesets which with prefix "AFFX" and "RPTR". One strange thing is that one probeset called "177968_at" is in s_pombe.msk but is NOT among the whole 10928 probesets! So the ...
written 11.9 years ago by Guiyuan Lei90
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Comment: C: Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
... Thank Jim and Caroline, I found that there are 5749 probesets in s_pombe.msk and 5028 probesets in s_cerevisiae.msk while there are total 10928 probesets on yeast2 chip. Does it mean that there are overlap between pombe and cerevisiae probesets? By the way, is there any smart way to use s_cerevis ...
written 11.9 years ago by Guiyuan Lei90
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Filter out pombe probeset from cerevisiae probesets for yeast2 Affymetrix chip
... Dear all, I am analyzing microarray data for Affymetrix yeast2 chip, I know that there are two organisms pombe and cerevisiae on this chip. I need to filter out pombe probesets. There are total 10928 probesets on yeast2 chip. How can I know which probeset is corresponding to pombe and which probese ...
microarray yeast2 written 11.9 years ago by Guiyuan Lei90 • updated 11.9 years ago by Caroline Lemerle20

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