Recently I found some datasets from GEO, but they are produced by illumina platform, and I don't know which kind of data should I download for further analysis? And the normal workflow for analysis?
Hi Kan,
You can use lumi package to do the analysis from the raw data (https://bit.ly/2C1lg2E).
Best,
Lei
On Dec 9, 2018, at 2:36 PM, kankejia0703 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote:
Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="<a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=DwMDaQ&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&s=kOBe5a88qFT2J4woQeOht7zZzkh2_3WV1unlQc1pJlE&e=">
User kankejia0703<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_18746_&d=DwMDaQ&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&s=Mz98OAuNl1ivxxPLQU5Y5LTko_Efsfx9o844QWBx9EE&e="> wrote Tutorial: download data from GEO Illumina platform<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_115934_&d=DwMDaQ&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&s=hzSEmxaCK3om4gF8CmjBCWCYP0tPRmLuK_4eMuCoLwc&e=">:
Hi, I am kan!
Recently I found some datasets from GEO, but they are produced by illumina platform, and I don't know which kind of data should I download for further analysis? And the normal workflow for analysis?
Download:
1. Download family-Series Matrix File(s)<https: urldefense.proofpoint.com="" v2="" url?u="ftp-3A__ftp.ncbi.nlm.nih.gov_geo_series_GSE57nnn_GSE57691_matrix_&d=DwMDaQ&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&s=If6cy5W1JOBjlZPVO4eXjQ4F82XgvgDWWy15xoEjWmY&e=">
or
2.Supplementary file-RAW.tar or _non-normalized_data.txt.gz
or
other data
Thanks!!
________________________________
Post tags: lumi, Tutorial
You may reply via email or visit download data from GEO Illumina platform<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_115934_&d=DwQDaQ&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&s=hzSEmxaCK3om4gF8CmjBCWCYP0tPRmLuK_4eMuCoLwc&e=">
To read and normalize the Illumina Beadchip data you can use:
> library(limma)
> x <- read.ilmn("GSE57691_non-normalized_data.txt.gz",probeid="ID_REF",expr="Sample ")
Reading file GSE57691_non-normalized_data.txt.gz ... ...
> y <- neqc(x)
Note: inferring mean and variance of negative control probe intensities from the detection p-values.
> group <- rep(c("smallAAA","largeAAA","AOD","Donor"),c(20,29,9,10))
Thank you very much!