Question: download data from GEO Illumina platform
0
gravatar for kankejia0703
6 months ago by
kankejia07030 wrote:

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!!

 

ADD COMMENTlink modified 6 months ago by lhuang730 • written 6 months ago by kankejia07030
Answer: download data from GEO Illumina platform
1
gravatar for lhuang7
6 months ago by
lhuang730
United States
lhuang730 wrote:
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 COMMENTlink written 6 months ago by lhuang730

Thank you very much!

ADD REPLYlink written 6 months ago by kankejia07030
Answer: download data from GEO Illumina platform
0
gravatar for Gordon Smyth
6 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

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 COMMENTlink modified 6 months ago • written 6 months ago by Gordon Smyth37k

Thank you very much!

ADD REPLYlink written 6 months ago by kankejia07030
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