expression pattern (heat map) of a list of probsets ids

Question

[zizigolu]

Hello friends,

I have an array (GSE63706), how I can have expression pattern of a list of targets genes (probsets ids) during different phase of experiment please?

Answer 1

[Sean Davis]

This can get you started, hopefully.

library(GEOquery)
gse = getGEO("GSE63706")[[1]] 
library(ComplexHeatmap)
sampleNames(gse)=pData(gse)$title
Heatmap(exprs(gse)[5000:5100,],cluster_columns = FALSE)

[zizigolu]

Thank you very much Sean,

Suppose that I have already downloaded GSE63706 and normalized that and I have a normalized text file now. and I have also a list of probesets (a text file of my interest probesets) in this array. I want to have a heat map showing the expression pattern of my interest probesets in this array, for example in this array I have 4 varieties and different tissues (rind and flesh) and phases (0,10,20,30,40 and 50 days after harvesting). heat maps showing the expression pattern of my probsets in varieties, tissues and phases I mean...when I entered above codes,

library(ComplexHeatmap)
Loading required package: grid
> sampleNames(gse)=pData(gse)$title
> Heatmap(exprs(gse)[5000:5100,],cluster_columns = FALSE)
Error in (function (x)  :
  REAL() can only be applied to a 'numeric', not a 'NULL'
Error in match(x, table, nomatch = 0L) :
  cannot pop the top-level viewport ('grid' and 'graphics' output mixed?)
Error: VECTOR_ELT() can only be applied to a 'list', not a 'integer'
Error in x$just :
  VECTOR_ELT() can only be applied to a 'list', not a 'character'
Error in valid.unit(x, units, recycle.data(data, FALSE, length(x), units)) :
  cannot pop the top-level viewport ('grid' and 'graphics' output mixed?)
>

From where you knew about my interest probesets please? I am just interested in expression pattern of those probesets

Help me more please

[Sean Davis]

What is the output of sessionInfo()?

[zizigolu]

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] GEOquery_2.34.0      Biobase_2.28.0       BiocGenerics_0.14.0
[4] ComplexHeatmap_1.0.0

loaded via a namespace (and not attached):
 [1] colorspace_1.2-6    rjson_0.2.15        circlize_0.2.5
 [4] GlobalOptions_0.0.7 RColorBrewer_1.1-2  RCurl_1.95-4.7
 [7] GetoptLong_0.1.0    shape_1.4.2         bitops_1.0-6
[10] XML_3.98-1.3
>

May you please help me to know expression pattern of my probesets based on varieties, tissues and phases?

[Sean Davis]

You could try replacing:

Heatmap(.....)

with

library(gplots)
heatmap.2(exprs(gse)[5000:5100,])

I'm not sure why your Heatmap() call does not work.