User: Vishal Thapar

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9 years ago
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Posts by Vishal Thapar

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Comment: C: IRanges merging query
... Thanks so much! It works great! -vishal On Fri, Nov 12, 2010 at 4:53 PM, Michael Lawrence wrote: > > > On Fri, Nov 12, 2010 at 12:18 PM, Vishal Thapar wrote: > >> Hi Kasper, >> >> Thank you for replying back. I had tried this earlier, but what I get is >> not ...
written 9.0 years ago by Vishal Thapar90
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Comment: C: IRanges merging query
... Thanks Herve'. That comes the closest to the answer but it still misses the values for which there is no pair on one of the sets. This is what I get: > punion(I1,I2) Error in .local(x, y, ...) : some pair of ranges have a gap within the 2 members of the pair. Use 'fill.gap=TRUE' to enforce th ...
written 9.0 years ago by Vishal Thapar90
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Comment: C: IRanges merging query
... Hi Kasper, Thank you for replying back. I had tried this earlier, but what I get is not what I expected. I sort of wanted to "merge" the ranges for each "chr" value. So I want to ranges in Chr1 to be merged separately from Chr2 and so on. What I Get is: > abc.chr=c("chr1","chr1","chr1","chr2"," ...
written 9.0 years ago by Vishal Thapar90
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IRanges merging query
... Hi All, I have a question about how to merge / have a union of 2 RangeData objects Say I have a rangeData1 head(rangeData1) RangedData with 6 rows and 0 value columns across 25 spaces space ranges | | 1 chr1 [ 101, 283] | 2 chr1 [ 704, ...
written 9.0 years ago by Vishal Thapar90 • updated 9.0 years ago by Kasper Daniel Hansen6.4k
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Comment: C: Suggestions for Chip-seq differential expression analysis
... Hi Mark, Thanks for your reply. I have used EdgeR for a paired comparison without a control but I haven't used it with one. Would you point me to a simple tutorial or just even the function in EdgeR that can help me do that? The way I understood edgeR was, that its for a paired comparison with repl ...
written 9.0 years ago by Vishal Thapar90
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Suggestions for Chip-seq differential expression analysis
... Hi, I wanted some suggestions for a Chip-Seq analysis that I am working on. I have ChIP-Seq data for 3 cell types, control, treatment1, treatment2. I have 2 replicates of each. I would like suggestions on how I could compare the 2 treatments to *each* other. One way to do this is to do a diff expre ...
written 9.0 years ago by Vishal Thapar90 • updated 9.0 years ago by Michael Lawrence11k
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GO categories in R for A. Thaliana
... Dear Listers, I had a small query. I am working with A. Thaliana and after some initial analysis I have a list of genes (2000 or so). I want to now classify them into GO categories. I know there are lots of web based tools to do this but I want to do this in R. Has anyone done this before ? (I am s ...
go arabidopsis thaliana written 10.4 years ago by Vishal Thapar90 • updated 10.4 years ago by Marc Carlson7.2k
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random positioning of duplicate spots
... Dear List, I had posted earlier about my problem but didn't get any response that could help so I am seeking your help again. I have duplicate spots on my nimblegen array that are position randomized so there is no order to their placement. In Limma when we call the duplicateCorrelation() function ...
go limma written 10.5 years ago by Vishal Thapar90 • updated 10.5 years ago by Peder Worning100
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limma: analyzing randomized duplicate spots on Nimblegen array
... Dear List, Hi! I am new to this list so here is a brief introduction: My name is Vishal and I am a post doc at Cold Spring Harbor Lab working on Chip-chip / seq data analysis. I have my background in computer algorithms so pardon me if I make some errors with my Biological and Statistical terminol ...
normalization limma written 10.5 years ago by Vishal Thapar90

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