download data from GEO Illumina platform
2
0
Entering edit mode
@kankejia0703-18746
Last seen 3.5 years ago

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)

or

2.Supplementary file-RAW.tar or _non-normalized_data.txt.gz

or 

other data

Thanks!!

 

lumi illumina human ht-12 v4 • 1.1k views
ADD COMMENT
1
Entering edit mode
lhuang7 ▴ 50
@lhuang7-7824
Last seen 2.4 years ago
United States
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="&lt;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_&amp;d=DwMDaQ&amp;c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&amp;r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&amp;m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&amp;s=Mz98OAuNl1ivxxPLQU5Y5LTko_Efsfx9o844QWBx9EE&amp;e="> wrote Tutorial: download data from GEO Illumina platform<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_115934_&amp;d=DwMDaQ&amp;c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&amp;r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&amp;m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&amp;s=hzSEmxaCK3om4gF8CmjBCWCYP0tPRmLuK_4eMuCoLwc&amp;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_&amp;d=DwMDaQ&amp;c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&amp;r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&amp;m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&amp;s=If6cy5W1JOBjlZPVO4eXjQ4F82XgvgDWWy15xoEjWmY&amp;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_&amp;d=DwQDaQ&amp;c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&amp;r=xL4Q6S12GMmYBezZBpx-1TUa8A7PiWnGousaWgWk2kI&amp;m=DKlHzBnnqEhRtUX4pZMVRXi96aPSgTE_1VxeS8LLuqk&amp;s=hzSEmxaCK3om4gF8CmjBCWCYP0tPRmLuK_4eMuCoLwc&amp;e=">
ADD COMMENT
0
Entering edit mode

Thank you very much!

ADD REPLY
0
Entering edit mode
@gordon-smyth
Last seen 6 hours ago
WEHI, Melbourne, Australia

See Sections 4.6 and 17.3 of the limma User's Guide:

http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

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))

Then you're ready to go with a limma analysis.

 

ADD COMMENT
0
Entering edit mode

Thank you very much!

ADD REPLY

Login before adding your answer.

Traffic: 467 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6