I am trying to get gene expression matrix for a list of genes I have for my list: Gene ID, Gene Symbol How can I get for each gene corresponding expression as array?? I suppose that I will have GENE_ID GENE_NAME SAMPLE_1 SAMPLE_2 ..... I am new in that, I don't know more details I am trying to study relation between diseases and genes(human) using gene expression as features. Thanks in advance.
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$\begingroup$ Are you working with a particular dataset? $\endgroup$– sjcockellJul 17, 2018 at 9:15
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$\begingroup$ I am using GEOquery library $\endgroup$– Eman IsmailJul 17, 2018 at 11:46
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The answer to this really depends on the type of data you're retrieving from GEO. Microarray data sets should have a normalised matrix of expression values uploaded as part of the entry. getGEO() from the GEOquery package will return a list of ExpressionSets - in many cases this list will have a length of 1. An ExpressionSet has an exprs() accessor for retrieving the expression matrix. An example (GSE76510, an Illumina HT12 v4 BeadArray dataset):
> library(GEOquery)
> gse76510 <- getGEO('GSE76510')
> names(gse76510)
[1] "GSE76510_series_matrix.txt.gz"
> class(gse76510$GSE76510_series_matrix.txt.gz)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"
> exprs(gse76510$GSE76510_series_matrix.txt.gz) %>% head
GSM2027280 GSM2027281 GSM2027282 GSM2027283 GSM2027284 GSM2027285 GSM2027286
ILMN_1343291 14.936287 14.983927 15.008199 14.830549 15.008199 14.789385 14.891532
ILMN_1343295 13.404168 13.329903 13.289727 13.222221 13.386299 13.240755 13.125056
ILMN_1651199 6.779805 7.189868 7.046952 6.962957 6.697924 6.850950 6.792647
ILMN_1651209 6.983803 6.769702 7.016746 6.954751 6.890472 6.982947 6.915671
ILMN_1651210 6.837042 6.999098 6.895225 6.944250 6.955914 6.917959 6.837368
ILMN_1651221 7.034363 7.025626 6.606457 6.977622 7.051120 6.971884 7.066445
GSM2027287 GSM2027288 GSM2027289 GSM2027290 GSM2027291
ILMN_1343291 14.891532 14.983927 14.848452 14.913474 15.008199
ILMN_1343295 13.240755 13.010757 13.525999 13.009661 12.998406
ILMN_1651199 6.786784 6.820451 6.851160 7.013586 6.864316
ILMN_1651209 6.983701 6.995199 7.270760 6.901377 6.950876
ILMN_1651210 6.804955 7.033074 6.894117 6.770691 7.000786
ILMN_1651221 7.003035 6.995199 7.050040 6.923861 6.929933
You will be able to filter out a list of required genes using the probe annotation (available in the appropriate annotation.db - in this case, for example, illuminaHumanv4.db).
If the dataset you're interested in is RNA-Seq, you're probably out of luck. There's currently no requirement on data submitters to provide expression estimates with an RNA-Seq dataset, so the ExpressionSet that GEOquery returns will most likely have an empty exprs slot.
Again, an example (GSE117133):
> gse117133 <- getGEO('GSE117133')
> exprs(gse117133$GSE117133_series_matrix.txt.gz)
GSM3271892 GSM3271893 GSM3271894 GSM3271895 GSM3271896 GSM3271897
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$\begingroup$ Sir, I am confused which dataset should I use that contains the list of my interest and help me in my model to predict relation between genes and diseases. Do you suggest to use GSE76510 (MY list is human proteins that included in DrugBank DB)?? Thanks in advance. $\endgroup$ Jul 19, 2018 at 10:54
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$\begingroup$ @EmanIsmail I’m not suggesting any specific dataset here - they are merely to illustrate how the functions work in R. You need to find a dataset in GEO that assays gene expression in your system of interest. $\endgroup$ Jul 19, 2018 at 11:17