User: khadeeja ismail

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Posts by khadeeja ismail

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Filtering by bead count
... Hi All, I need to filter IlluminaHM 450 data based on bead count. The data is as a methyLumiSet and I cannot find out how to obtain the bead counts. Would be great if some one can help. (There seems to be a function in minfi, but trying to avoid reading the data again as a minfi object.) Thank you ...
methylumi written 2.5 years ago by khadeeja ismail400 • updated 2.5 years ago by Mike Smith2.8k
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Comment: C: QQ plot 450k data
... Very helpful. Thank you, Jim, Martin and John. Best, Khadeeja On Tuesday, May 20, 2014 8:28 PM, James W. MacDonald wrote: Hi Khadeeja, I don't think you can conclude much at all from a QQ plot, other than the obvious that the observed p-values don't follow the expected distribution. There can ...
written 4.2 years ago by khadeeja ismail400
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Comment: C: QQ plot 450k data
... Thank you very much. I was suggested QQ plots to look for biases in two different analysis. One seem to have a uniform distribution while the other seem to deviate much. Probably due to different global methylation profiles? Can I conclude from it that there is a bias? Thanks again, Khadeeja O ...
written 4.2 years ago by khadeeja ismail400
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QQ plot 450k data
... Hi All, What would be the right distribution to use as expected p values in a QQ plot for results from 450k analysis? I have been searching, but not able to find in mentioned anywhere. Thanks in advance, Khadeeja [[alternative HTML version deleted]] ...
written 4.2 years ago by khadeeja ismail400 • updated 4.2 years ago by James W. MacDonald47k
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Comment: C: Genome Browser and R
... Thanks for the information. It had been very helpful. Best regards, Khadeeja On Sunday, October 27, 2013 7:05 AM, Michael Lawrence wrote: If it's in UCSC, you can probably find the right track in AnnotationHub. Michael On Sat, Oct 26, 2013 at 5:02 PM, khadeeja ismail wrote: Hi Michael, ...
written 4.8 years ago by khadeeja ismail400
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Answer: A: Genome Browser and R
... Hi Michael, We obtained a list of about 80 probes from differential methylation analysis, mapping to genes associated with the phenotype we are studying. One of my colleagues had been looking at the probes one by one on genome browser, to see if the CpG site was anywhere near a regulatory region, ...
written 4.8 years ago by khadeeja ismail400
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Comment: C: Genome Browser and R
... Hi, Thanks for a lot of help and an interesting discussion. IT has been very useful. I ran the code and was able to get the overlaps for the histone markers, but still need to try the same for the tnx, and dnase etc. Hope no problems pop up. Btw, I meant 100bp, and not 100kb. Hector, I had some pro ...
written 4.8 years ago by khadeeja ismail400
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Comment: C: Genome Browser and R
... Thanks much for the help. Will have a go and let you know. I have about 80 probes, from many different genes. I'm not sure if they can be summarized, but sure it's worth having a look. BR, Khadeeja On Thursday, October 24, 2013 8:53 PM, Martin Morgan wrote: On 10/24/2013 09:37 AM, khadeeja ...
written 4.8 years ago by khadeeja ismail400
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Genome Browser and R
... Hi, I am working  with some 450k array probes which I need to look up in Geneome browser to see in which type of areas these probes are located in.  For example, if the CpG site (+/- 100kb) overlaps with any of the following in the GM12878 track. Layered H3K27Ac Layered H3K4Me1 Layered H3K4Me3 T ...
rtracklayer written 4.8 years ago by khadeeja ismail400
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Crlmm package
... Dear All, I'm trying to preprocess data from Illumina's GoldenGate assay, using the crlmm package. I tried to follow the userguide but keeps getting an error after the quantile normalization step. My output is as shown below. > cnSet <- genotype.Illumina(sampleSheet=samplesheet,arrayNames ...
snp annotation normalization crlmm written 5.5 years ago by khadeeja ismail400 • updated 5.5 years ago by Matthew Ritchie730

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