User: krishna312

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krishna3120
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Posts by krishna312

<prev • 8 results • page 1 of 1 • next >
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minfi: filtering of probes
... Hi, I am quite new to methylation data analysis. I am using minfi for illumina 450k data analysis. I would appreciate if someone would answer the following question:  I want to exclude probes with a) detection P-value > 0.01, and b) intensity summarized with < 3 beads. I think this step shou ...
minfi written 2.4 years ago by krishna3120
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Comment: C: lumi: how to get number of beads information?
... Thanks for pointing that out! However, I am still looking for answer regarding getting information about number of beads used for summarizing intensities in lumi (analogous to "nbeads <- assayData(RGset)$NBeads in minfi"). best wishes, Krishna ...
written 2.4 years ago by krishna3120
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lumi: how to get number of beads information?
... Hi, I would like to get number of beads used to summarize intensity in infinium methylation 450k data and remove intensities based on less than 3 beads. I can easily get that information using minfi as follows, nbeads <- assayData(RGset)$NBeads How can do that in lumi? Further, I noticed tha ...
lumi minfi written 2.4 years ago by krishna3120 • updated 2.4 years ago by Kasper Daniel Hansen6.4k
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polyester: adding noise to RNASeq counts?
... I have a RNASeq raw count data. I want to generate different versions of the count data with varying level of random noise for a method evaluation. For example, the data with highest level of noise will have fewest differentially expressed genes and vice-versa. I estimated the parameters of the ori ...
rnaseq polyester written 2.4 years ago by krishna3120 • updated 2.4 years ago by Alyssa Frazee200
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Voom: estimation of mean-variance relationship with gene expression data normalized with methods other than cpm
... Hi, I understand that voom normalizes the raw count data to log2 cpm data and then estimates the mean-variance relationship from the normalized data. I want to know if there is strong bonding between log2 cpm data and estimation of mean-variance relationship? In other words, will I get sensible re ...
limma voom written 2.6 years ago by krishna3120 • updated 2.6 years ago by Gordon Smyth35k
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Comment: C: Gene set analysis with CAMERA
... Thanks Aliaksei! That helped!! ...
written 4.2 years ago by krishna3120
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Answer: A: Gene set analysis with CAMERA
... Thanks a lot Aliaksei! That helped!! ...
written 4.2 years ago by krishna3120
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Gene set analysis with CAMERA
... Hi, I would be thankful for replies to my question related to gene set analysis with camera. Following is the problem: Consider the example given on camera help page (?camera). y <- matrix(rnorm(1000*6),1000,6) design <- cbind(Intercept=1,Group=c(0,0,0,1,1,1)) # First set of 20 genes are g ...
limma camera gene set analysis written 4.2 years ago by krishna3120 • updated 3.6 years ago by Gordon Smyth35k

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For Gene set analysis with CAMERA

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