I know this may be a very basic query. I import the data for the expression.table in as a .txt file and cannot transpose in excel due to column limits (38000 genes).
If you have any suggestions they are very welcome!
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The expression.table is just a file name. The file is not read until after the RNA.norm() function is run (so, you can't transpose the file that way). Instead, you would need to transpose it by reading the file via read.table() and then writing the transposed table via write.table().
That said, those seem like very high numbers. For example, a human genome should have ~20,000 genes (and perhaps ~40,000 transcripts, if you focus on transcript measurements). The largest RNA-Seq datasets that I know of have less than 1-2 thousand samples. So, regardless of which is defined on columns versus rows, I wouldn't expect more than a 50,000 x 2,000 table.
So, can you please answer the following questions:
1) What organism are you studying?
2) How many samples are you trying to analyze?
3) How are you creating the input file for sRAP (specifically, how are you creating the expression table)?
Thanks,
Charles
Last edit: Charles Warden 2014-03-24
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2014-04-02
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2015-09-03
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Hello, This is quite a basic question but when I run
expression.mat = RNA.norm(expression.table, project.name, project.folder) using my own data
I get the following error
Error in WriteXLS("norm.expr", ExcelFileName = xlsfile) :
One or more of the data frames named in 'x' exceeds 1,048,576 rows or 16,384 columns
I know I need to transpose my data to have it in the correct format (i.e. genes as columns, samples as rows), however when I run
CETPLexpression.mat = RNA.norm(t(CETPLexpr.table), project.name, project.folder)
I get the same error.
I know this may be a very basic query. I import the data for the expression.table in as a .txt file and cannot transpose in excel due to column limits (38000 genes).
If you have any suggestions they are very welcome!
Hi,
The expression.table is just a file name. The file is not read until after the RNA.norm() function is run (so, you can't transpose the file that way). Instead, you would need to transpose it by reading the file via read.table() and then writing the transposed table via write.table().
That said, those seem like very high numbers. For example, a human genome should have ~20,000 genes (and perhaps ~40,000 transcripts, if you focus on transcript measurements). The largest RNA-Seq datasets that I know of have less than 1-2 thousand samples. So, regardless of which is defined on columns versus rows, I wouldn't expect more than a 50,000 x 2,000 table.
So, can you please answer the following questions:
1) What organism are you studying?
2) How many samples are you trying to analyze?
3) How are you creating the input file for sRAP (specifically, how are you creating the expression table)?
Thanks,
Charles
Last edit: Charles Warden 2014-03-24