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This article Xiaobian for you to introduce in detail the "agilent expression profile chip annotation information extraction method", the content is detailed, the steps are clear, the details are handled properly, I hope that this "agilent expression profile chip annotation information extraction method" article can help you solve doubts, following the editor's ideas slowly in depth, together to learn new knowledge.

Non-standard annotation information extraction of expression profile chip

The main results are as follows: 1. The agilent expression profile chip in GEO database is often more personalized than its design, and many chip types are involved. the two-color chip of Cy5/Cy3 or the monochrome chip that only uses Cy3 are confused in data, but the file format of GPL information provided in GEO is quite different from that of affymetrix and illumina, although the format is neat. It is not fully standardized (as opposed to downloading chip annotation files directly using GEOquery).

2. When downloading standardized data directly, errors often occur in downloading the corresponding GPL chip platform information using GEOquery, or in the process of extracting information. This paper provides a method to obtain the agilent expression chip GPL information, which is relatively neat and uniform in format. In the process of standardizing the original data of the chip, we can directly obtain the annotation information: the corresponding relationship between probes and genes.

3. Here we only take the single-channel chip data as an example: the case data GSE83902 reads the data based on the limma packet and carries out pre-processing. After standardization, the obtained result is an EList object, which contains the corresponding relationship between the probe and the gene. After averaging the probe detection value repeated in the chip, an EList is obtained (here the returned result after taking the mean value is represented by the averEList vector):

Check the corresponding genes information in averEList. This matrix includes each column of information, including the following information related to probes ProbeName and GeneName, as well as description information, and then extract and save:

> colnames (averEList$genes) [1] "Row", "Col", "Start", "Sequence", "ProbeUID" [6], "ControlType", "ProbeName", "GeneName", "SystematicName"Description" > Probe=averEList$genes [, c ("ProbeName", "GeneName", "SystematicName", "Description")] > head (Probe) 5) ProbeName GeneName SystematicName1 GE_BrightCorner GE_BrightCorner GE_BrightCorner2 DarkCorner DarkCorner DarkCorner4 A_23_P117082 HEBP1 NM_0159875 A_33_P3246448 KCNE4 NM_0806716 A_33_P3318220 BPIFA3 NM_178466 Description1 2 4 Ref | Homo sapiens heme binding protein 1 (HEBP1) MRNA [NM_015987] 5 ref | Homo sapiens potassium voltage-gated channel, Isk-related family, member 4 (KCNE4), mRNA [NM_080671] 6 ref | Homo sapiens BPI fold containing family A, member 3 (BPIFA3), transcript variant 1, mRNA [NM_178466]

Note: the column names involved in the matrix that can be obtained by EList$genes in the EList results obtained by different chips are different, which should be treated in detail.

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