[BioC] DEGseq help

[Tina Asante Boahene]

Hi all,

I am trying to do some analysis using the DEGseq package however I am encountering some problems.

I am using the DEGseq vignette but I can not read my data in the same format.

My data is in the format MA.subsetA.

I am actually using the Marioni et al dataset which is mad up of the following;

names(MA.subsetA)
[1] "M"     "genes"

 dim(MA.subsetA)
[1] 22490    10

MA.subsetA[1:3,]
An object of class "MAList"
$M
   R1L1Kidney R1L2Liver R1L3Kidney R1L4Liver R1L6Liver R1L7Kidney R1L8Liver
10          0         0          0         0         0          2         1
15          4        35          7        32        31          3        29
17          0         2          0         0         0          1         0
   R2L2Kidney R2L3Liver R2L6Kidney
10          4         0          3
15          6        34          7
17          1         0          0

$genes
     EnsemblGeneID Chr GeneStart GeneEnd Status ExternalID
10 ENSG00000209342   1    554815  554882  NOVEL           
15 ENSG00000209350   1    557859  557930  NOVEL           
17 ENSG00000209352   1    558707  558776  NOVEL 


I want to be able to use the method "LRT"  to analyse Differentially expressed genes with a false discovery rate  <0.01 (FDR<1%).

Since I can not read the dataset into R I cant do this.

Ideally I want to be able to get some results which incorporate the gene ID (EnsemblGeneID) and the various libraries (eg:R1L1Kidney, R1L2Liver, R1L3Kidney, etc ),
 because it will make the analysis much easy.

However, I have noticed that within the DEGseq vignette the text file "GeneExpExample5000.txt" is used I want to find out whether it incorporate all the other libraries.
This is because I am going to use the results obtained from the DE genes from this package and that obtained from baySeq package using the Poisson approach to do some comparison.
Hence my reason for having all the dataset being representative of the analysis to follow in order to avoid any bias.


Thank you . 


Kind Regards

Tina