How to get colData with GEOquery to prepare for DEseq2
1
0
Entering edit mode
Yugang • 0
@3cef1a12
Last seen 12 days ago
China

Hi guys,

I tried to get the colData from the GSE dataset I have downloaded with GEOquery. I have two problems to solve.

  1. How to get the counts table from the dataset?
  2. How to prepare for the colData that the DEseq2 package asks for?

Here's what I have done.

First I downloaded the dataset in the matrix form and transform into expression set to have a look at the table.

gse <- getGEO("GSE7765", GSEMatrix = TRUE) 
show(gse)

#take a look at the metadata
metadata<-pData(gse[[1]])
metadata[,1:5]
colnames(metdata)
# thus I know the group division

#then I turn the sample into the expression set
eset = exprs(gse[[1]])
dim(eset)
head(eset)

The doc says that if I download the matrix form, I should get the expression set. I tried head(gse[[1]]) but failed to see the table.

Then after the trans, the table shows but it's not counts table, so I have to re-download the dataset with the soft format.

rm(list = ls())
gse <- getGEO("GSE7765",GSEMatrix = F) 
show(gse)
GSMList(gse)[[1]]

Then I look at the first sample and get the column description ** Column Descriptions ** Column Description 1 ID_REF = 2 VALUE value 3 ABS_CALL present/absent 4 DETECTION P-VALUE 0.05

So I still dont get the counts table that I need for the DEseq2 package. Neither do I know how to prepare for the colData.

sessioninfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pheatmap_1.0.12     GEOquery_2.64.0     Biobase_2.56.0     
[4] BiocGenerics_0.42.0

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-3  pillar_1.7.0        compiler_4.2.0     
 [4] BiocManager_1.30.17 R.methodsS3_1.8.1   R.utils_2.11.0     
 [7] base64enc_0.1-3     tools_4.2.0         digest_0.6.29      
[10] uuid_1.1-0          gtable_0.3.0        jsonlite_1.8.0     
[13] evaluate_0.15       lifecycle_1.0.1     tibble_3.1.6       
[16] pkgconfig_2.0.3     rlang_1.0.2         IRdisplay_1.1      
[19] cli_3.3.0           DBI_1.1.2           curl_4.3.2         
[22] IRkernel_1.3        fastmap_1.1.0       xml2_1.3.3         
[25] repr_1.1.4          dplyr_1.0.9         generics_0.1.2     
[28] vctrs_0.4.1         hms_1.1.1           grid_4.2.0         
[31] tidyselect_1.1.2    glue_1.6.2          data.table_1.14.2  
[34] R6_2.5.1            fansi_1.0.3         limma_3.52.0       
[37] pbdZMQ_0.3-7        tidyr_1.2.0         purrr_0.3.4        
[40] readr_2.1.2         tzdb_0.3.0          magrittr_2.0.3     
[43] scales_1.2.0        ellipsis_0.3.2      htmltools_0.5.2    
[46] assertthat_0.2.1    colorspace_2.0-3    utf8_1.2.2         
[49] munsell_0.5.0       crayon_1.5.1        R.oo_1.24.0

I'm new to this. Thanks for your help, and I would appreciate it if you recommend some materials to learn about RNA seq analysis.

GEOquery DEseq2 • 94 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

That submission is from some Affymetrix HG-U133A and B arrays. You won't get counts, and you shouldn't use DESeq2 to analyze those data. You could use limma however.

0
Entering edit mode

Thanks. I'll look up for the differences between DEseq2 and limma. I realized that limma is installed with DEseq2.

ADD REPLY

Login before adding your answer.

Traffic: 147 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6