Analysis of Agilent Microarray one-color | SurePrintG3 Human Gene Expression v2 8x60k

Question

[g.felio.rolo]

Hi everyone,

It is the first time I work with this kind of data. The information of my data is the following:

• SurePrintG3 Human Gene Expression v2 8x60k microarray (Agilent ref.G4851B) 83 samples (47 primary tumors más 36 metastasis)

I need to do the preanalysis (Normalization and do some basic analysis for microarray data) and also performe the tumor purity with Estimate package or some similar package. I am trying to use some scripts for doing the preanalysis with lima in R such as:

A: How to process (seems) Agilent microarrry data?

Single-color Agilent array analyzing in R

This examples are made for specific agilent kits, so I am not sure to use it or modify some part of the scripts

Moreover I have the microarray data in .txt files and a target file with the following info:

FileName    Sample_Type
2701    PT
2708    PT
2710    PT
2711    PT
2712    PT
2713    M1
2714    M1

PT: primary tumor M1: Metastasis

Thanks in advance,

Answer 1

[Kevin Blighe]

Hi, there seems to be some information missing from your post.

For Agilent one- and two-colour arrays, I have posted generic code that can be used:

• One-colour / Single-channel: A: How to process (seems) Agilent microarrry data?
• Two-colour / Two-channel: A: build the expression matrix step by step from GEO raw data

Kevin

[g.felio.rolo]

Hi Kevin, Thanks for your reply. I was following your script but I have some doubts:

In my case, the analysis was made with "SurePrintG3 Human Gene Expression v2 8x60k microarray" So, in the follwing part of your script, should I change the name of attributes to: 'agilent_wholegenome_8x60k_v2' ?

annotLookup <- getBM( mart = mart, attributes = c( 'agilent_wholegenome_4x44k_v1', 'wikigene_description', 'ensembl_gene_id', 'entrezgene', 'gene_biotype', 'external_gene_name'))

Thanks again, G. Phil

[Kevin Blighe]

Hey, for the 8x60k v2 you can use:

# agilent_sureprint_g3_ge_8x60k_v2
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_sureprint_g3_ge_8x60k_v2',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'external_gene_name'))

[g.felio.rolo]

Hi Kevin, thanks again. I used the function listAttributes(mart) and it display all options.

However, I get the following warning:

Error in getBM(mart = mart, attributes = c("agilent_sureprint_g3_ge_8x60k_v2", : Invalid attribute(s): entrezgene Please use the function 'listAttributes' to get valid attribute names

I think the proper attribute is "entrezgene_id". Please correct me if I'm wrong.

On other hand, I'm also interested in a normalized input in order to performe The tumor purity with ESTIMATE package. Please, if you know any way to create this input, It would help me a lot.

Thanks again,

G. Phil

[Kevin Blighe]

Yes, please use entrezgene_id. This was modified internally at Ensembl within the past couple of months.