User: linouhao

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linouhao0
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Posts by linouhao

<prev • 28 results • page 1 of 3 • next >
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tool for calculate tumor-only sample purity of wgs or wes
... hi, is there a tool to calculate tumor only samle purity of wgs or wes? thanks a lot ...
genome next-gen written 2 days ago by linouhao0
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Comment: C: negative geo value analysis
... thanks a lot, I do not have much experience here, and can not handle the normalization well, either normalwithinarrays and normalbetweenarrays. the negative values here maybe not because of log, but also of backgroud substraction, because many gse also do rma and log, but no negative values. do you ...
written 9 weeks ago by linouhao0
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Comment: C: series_matrix.txt in GEO are they always the normalized values?
... thanks a lot, how did you come to this conclusion,just because the median of 712058 and 712060 is much higher? ...
written 9 weeks ago by linouhao0
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Comment: C: Single-color and two color Agilent array analyzing in R
... in the limma, it has two different part of two color, one is direct two-color, do you know the meanning ...
written 9 weeks ago by linouhao0
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Comment: A: series_matrix.txt in GEO are they always the normalized values?
... https://ibb.co/B2RV1CD ![picture][1] is this comparbale? thanks a lot code copy from you library(Biobase) library(GEOquery) gset <- getGEO("GSE28739", GSEMatrix =TRUE, getGPL=FALSE) if (length(gset) > 1) idx <- grep("GPL6480", attr(gset, "names")) else idx <- 1 ...
written 9 weeks ago by linouhao0 • updated 9 weeks ago by zx87549.7k
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Comment: C: Why some microarray data have negative value? How to fix it?
... hi, you said negative value is normal, and can I use limma to analyse it directly, because someone else said that the negative value should be removed because of backgroud substraction and log transform and here do you think the picture you showed is comparable or not? thanks a lot ...
written 9 weeks ago by linouhao0
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negative geo value analysis
... hi, GSE55542 is a geo data, for example, one chip in it https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1338936 it has negative value, so can I use limma to analyse this data? thanks a lot ...
microarray written 10 weeks ago by linouhao0 • updated 9 weeks ago by zx87549.7k
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Comment: C: CNVkit - how many normal samples do I need for the pooled normal reference?
... so how should we select the normal samples, is there any suggestions, I noticed that you mentioned the bam files size, so is there any concrete methods I also noticed thta you mentioned metrics These statistics help quantify how “noisy” a sample is and help to decide which samples to exclude from a ...
written 3 months ago by linouhao0
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Comment: C: CNV callers for WES data
... not a good choice, cnvkit can do this, but the result is not good ...
written 3 months ago by linouhao0
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Comment: C: Noisy CNV background in old FFPE sample
... so is there any qc criteria for cnvkit of detecting wes, wgs, tr sequence, for example depth? because we often talk about low quality, but there often saying no concrete value for these. for example, you said larger bins for low quality FFPE,but what the value ,wes target bin to be 2000 instead of 2 ...
written 3 months ago by linouhao0

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