User: sylvia

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sylvia10
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Posts by sylvia

<prev • 19 results • page 1 of 2 • next >
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Comment: C: dba.count with pre-defined regions
... Hi Rory, Sorry, and one more thing, is it normal that not all the peaks having 201bp w after using summits function? Best, Sylvia ...
written 4 weeks ago by sylvia10
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Comment: C: dba.count with pre-defined regions
... Hi Rory, For the second TF.counts do you mean TF.counts <- dba.count("TF.counts", peaks = NULL, summits=100)? or I should still use TF.peaks? This is really helpful! Thanks a lot. Best, Sylvia ...
written 4 weeks ago by sylvia10
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Comment: C: dba.count with pre-defined regions
... Hi Rory, Thanks for the quick reply, It works now! One more naive question, if I used a pre-defined region is there still a way to re-center each peak around the point of greatest enrichment, like the summit function? so I can use a shorter sequence for motif finding? Best, Sylvia ...
written 5 weeks ago by sylvia10
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Comment: C: dba.count with pre-defined regions
... Thanks Rory! Just sent. Best, Sylvia ...
written 5 weeks ago by sylvia10
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dba.count with pre-defined regions
... Hi, I'm trying to use dba.contrast and dba.analyze to find differential binding sites within specific regions (ie  promoter region ranging from 1000bp upstream of TSS and 500 bp downstream of TSS for a set of genes). I realized that dba.count can use pre-defined regions with the peaks argument so I ...
chipseq diffbind dba.count dba written 5 weeks ago by sylvia10 • updated 5 weeks ago by Rory Stark2.2k
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Comment: C: How to use cdf version20 with oligo package
... Hi James, I might have load affy package at the same time and didn't specify which rma to use and when I read the arguments for rma from oligo package the object is : Exon/HTA/Expression/Gene/SnpCnv-FeatureSet so I thought it doesn't take GenericFeatureSet! Sorry for the confusion, now it works! T ...
written 23 months ago by sylvia10
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How to use cdf version20 with oligo package
... HI Sorry if this is obvious, but I was wondering how do people use custom cdf with oligo package ? I downloaded the cdf version 20 from column 'O' for the hugene20 st array (pd.hugene20st.hs.entrezg_20.0.0.tar.gz) and installed the package and I tried to do something like this: dat <- read.cel ...
cdf oligo written 23 months ago by sylvia10 • updated 23 months ago by James W. MacDonald45k
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Comment: C: HTA 2.0 ST array annotation
... Hi James, Thank you for your time! I'll take a look at TxDb. Best, Sylvia ...
written 24 months ago by sylvia10
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Comment: C: HTA 2.0 ST array annotation
... I see, thanks for the quick reply! I was a bit concerned cause some of the same genes in the hta20sttrnascriptcluster.db have different chromosome locations and when I checked NCBI I realized none of the location match to the NCBI chromosome location for that gene. For example, Entrez gene ID: 10087 ...
written 24 months ago by sylvia10
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Comment: C: HTA 2.0 ST array annotation
... Hi James, I just have a follow up question, I was wondering what build of the genome was the annotation based on. Is it hg18 or hg19? Best, Sylvia ...
written 24 months ago by sylvia10

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