how many Microarray types do we have?

Question

[Mo]

There are so many review papers published on this topic at least in Nature review and each has its own category. how many DNAmicroarray do we have ? what are the advantages and disadvantages of them?

Can we distinguished them into two groups like cDNA and oligonucleotide microarrays?

[Devon Ryan]

Err, a cDNA is an oligonucleotide...

[Mo]

@Devon Ryan I agree since in cDNA ,the probes can be oligonucleotides, cDNA, or small fragments of PCR products that correspond to mRNAs. on the other hand In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames which is normally refers to a specific technique like Affymetrix etc. However, how would you classify them? this is my question

Answer 1

[Neilfws]

There are probably many ways to classify microarray "types"; I don't know that any of them are very meaningful or useful.

You could start by visiting NCBI GEO Platforms browser, from where you can export data (in chunks of 5000 records). I loaded that data into R and ran table() over the "Technology" column, for this result.

> as.data.frame(table(platforms$Technology))
                                 Var1 Freq
1                                        1
2                            antibody   24
3          high-throughput sequencing 1908
4             in situ oligonucleotide 5524
5  mixed spotted oligonucleotide/cDNA   16
6                                MPSS   18
7                                  MS   17
8               oligonucleotide beads  223
9                               other  164
10                             RT-PCR  268
11                        SAGE NlaIII   67
12                          SAGE RsaI    1
13                         SAGE Sau3A    4
14                              SARST    2
15                   spotted DNA/cDNA 2859
16            spotted oligonucleotide 2831
17         spotted peptide or protein  105