Question: GEO study selection for analysis in R
0
gravatar for 786
2.9 years ago by
78650
78650 wrote:

Hi I just want to ask that when we are going to analyze micro-array data in R then can we consider those studies in which disease and control states of samples are not defined?? Please help me out it'll be very helpful.

geo2r R geo • 932 views
ADD COMMENTlink modified 2.1 years ago by ugandhar.ch110 • written 2.9 years ago by 78650
2

Could you please post the GEO number where the state is not defined? Because generally it is a required information for GEO data sets.

ADD REPLYlink written 2.9 years ago by eldronzhou350

GSE54279 in this study control and diabetic aren't taken properly. How to find the groups of this series on the basis of HbA1c levels??

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by 78650

I'm not sure whether the author include the diabetic samples in this dataset. The author intended to show that CD59 is highly expressed in the human pancreatic islets and silencing CD59 (intracellular) can suppress insulin secretion. From Figure 1A we can see that CD59 is highly expressed in the islets, implying that all the samples were from normal people. Otherwise they should not pool the expression pattern from two different groups without comparision. Also, the authors did not mention patients anywhere in the article. Thus I think there is only one group in the data set. You may e-mail the author for direct clarification.

ADD REPLYlink written 2.9 years ago by eldronzhou350

Thank u so much fr your guidance :)

ADD REPLYlink written 2.9 years ago by 78650
3
gravatar for Shicheng Guo
2.9 years ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

How to get the sample information?

library("GEOquery")
GSE56851 <- getGEO("GSE56851",destdir="/home/sguo/monod/data/geo")
data <- as.data.frame(exprs(GSE56851[[1]]))
phen <- pData(phenoData(GSE56851[[1]]))

Then you can find all the sample information in phen, as Eldon said, these information is essential when you upload array to GEO

ADD COMMENTlink written 2.9 years ago by Shicheng Guo7.4k
1
gravatar for ugandhar.ch1
2.1 years ago by
ugandhar.ch110
ugandhar.ch110 wrote:

i am able to get phenodata information from GSE8977, But i am bit confused how to create a text file? how can i create COVDESC FILE ?

ADD COMMENTlink written 2.1 years ago by ugandhar.ch110
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