How to get the expression data of each gene from the ArrayExpress database.

Question

[zihuguo1986]

I want to get the different expressed MicroRNA between the gastritis and normal samples. So I download all the MAGE-TAB data which was provided in this link, and I want to obtain the different expressed MicroRNAs from this study. This study contain 5 files as shown bellow

Investigation description  E-TABM-434.idf.txt
Sample and data relationship  E-TABM-434.sdrf.txt
Raw data (1)                 E-TABM-434.raw.1.zip
Array design                 A-MEXP-258.adf.txt
R ExpressionSet             E-TABM-434.eSet.r

In the first step I used this code to get the data

ETABM434<-ArrayExpress("E-TABM-434")

but I got an error. the error message was show below

Unpacking data files
ArrayExpress: Reading pheno data from SDRF
ArrayExpress: Reading data files
Error in getDataColsForAE1(path, files) : "GenePix:% > B635+1SD" 
"GenePix:% > B635+2SD" 
"GenePix:Autoflag" 
"GenePix:B Pixels" 
"GenePix:B635" 
"GenePix:B635 CV" 
"GenePix:B635 Mean" 
"GenePix:B635 Median" 
"GenePix:B635 SD" 
"GenePix:Circularity" 
"GenePix:Dia." 
"GenePix:F Pixels" 
"GenePix:F635 % Sat." 
"GenePix:F635 CV" 
"GenePix:F635 Mean" 
"GenePix:F635 Mean - B635" 
"GenePix:F635 Median" 
"GenePix:F635 Median - B635" 
"GenePix:F635 SD" 
"GenePix:F635 Total Intensity" 
"GenePix:Flags" 
"GenePix:Log Ratio (635/2)" 
"GenePix:Mean of Ratios (635/2)" 
"GenePix:Median of Ratios (635/2)" 
"GenePix:Normalize" 
"GenePix:Ratio of Means (635/2)" 
"GenePix:Ratio of Medians (635/2)" 
"GenePix:Ratios SD (635/2)" 
"GenePix:Rgn R2 (635/2)" 
"GenePix:Rgn Ratio (635/2)" 
"GenePix:SNR 635" 
"GenePix:Sum of Means (635/2)" 
"GenePix:Sum of Medians (635/2)" 

In addition: Warning message:
In download.file(url, filedest, mode = "wb") :
  downloaded length 532480 != reported length 859427
ArrayExpress: Reading feature metadata from ADF
Read 50 items
Error : object 'raweset' not found

So I tried to load the the R ExpressionSet

load("E:/work/META/different expression/E-TABM-434.eSet.r")

I got a NChannelSet object named study. Can I get the expression data of each MicroRNA from this object, and further more get the different expressed MicroRNA between the gastritis and normal samples? I know how to get the expression data from the ExpressionSet class, "exprs" command will be ok, but I have no idea with NChannelSet class. Any suggestion will be appreciated. Thank you very much!

Answer 1

[komal.rathi]

You can get expression using the assayDataElement function:

load("E-TABM-434.eSet.r")
expr = assayDataElement(study,"G")

Read this paper to get the sense of how to import an ArrayExpress dataset into R. Read this manual to know what an NChannel object is. Also, read Section 8 of this manual on how to identify differentially expressed genes from an ArrayExpress dataset.

[zihuguo1986]

Thank you very much, it works