Microarray

Question

[Mostafa]

Hi best dear

I am researching on the Microarray Data, i have faced with some problems: I gave the microarray data and for analysing i need Gene:ID

How can i convert ProbeID to Gene ID?

my address: [e-mail] Thanks Mostafa

Answer 1

[Kevin Blighe]

Hi Mostafa, some questions for you:

1. Which manufacturer made the array that you are using: Affymetrix, Agilent, or Illumina?
2. Which array type is it? - for example, Affymetrix Human Gene 1.0 ST Array, Illumina HumanHT-12 v3, et cetera
3. Can you please paste some of the Probe IDs?

[Mostafa]

hi dear I used Affymetrix data of Hordeum vulgare

for example: Probe ID: Contig17412_at HU10K22u_s_at Contig15844_at Contig8247_at Contig16848_at Contig996_s_at Contig3286_s_at Contig5665_at HVSMEa0020P01f_at Contig3811_at Contig3901_s_at Contig1205_s_at Contig23549_at Contig6204_at rbaal38l09_s_at Contig3873_at Contig3875_s_at Contig3426_at Contig10029_at Contig18698_at Contig19438_at Contig9531_at Contig16113_at Contig4024_at Contig590_s_at Contig6654_at Contig8416_at Contig3287_x_at Contig3057_s_at Contig11343_at Contig8305_at Contig18277_at Contig12508_s_at Contig16542_at HS09O21u_at Contig14742_at Contig11773_at Contig5527_at Contig4056_s_at Contig2720_at

[Kevin Blighe]

Hordeum vulgare? - wonderful, I know it well.

The annotation is not great for this; however, you can retrieve the NetAffx file and use that in a customised fashion, if you wish.

1. Go here: http://www.affymetrix.com/support/technical/byproduct.affx?product=barley1
2. Download: http://www.affymetrix.com/Auth/analysis/downloads/na36/ivt/Barley1.na36.annot.csv.zip
3. Unzip the file's contents
4. In R:

.

annot <- read.csv('Barley1.na36.annot.csv', skip = 13, header = TRUE)
annot[grep('Contig3901_s_at', annot$Probe.Set.ID),]

You can also try these methods to retrieve more annotation:

• https://support.bioconductor.org/p/131067/#131118
• https://support.bioconductor.org/p/130727/#130733

[Mostafa]

very thanks dear