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Old 01-17-2013, 04:35 AM   #1
Carmen
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Location: Italy

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Default DESeq error

Hi,
I am trying to analyze my RNA-seq data with DESeq
my count_table appear as follow

C1_count C2_count C3_count T1_count T2_count T3_count
1 fdoG 1898 2819 2159 2713 3388 3273
2 fdoH 364 596 470 552 667 643
3 fdoI 163 257 215 237 302 273
4 fdhE 324 537 442 406 596 607
5 selA 289 587 551 553 639 618
6 SMa0013 119 256 221 238 302 251


when I try

>cds <- newCountDataSet(count_table, conds)

I get the following error message:
Error in round(countData) : Non-numeric argument to mathematical function

Does anyone help me?

Thanks
Carmen
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Old 01-17-2013, 04:59 AM   #2
chadn737
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Default

It looks like how your counts table is set up, that your gene names are being seen as a column of read counts. Since these are characters, not numbers, DESeq doesn't know how to use them. You need to make those gene names the row names in R.
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Old 01-17-2013, 05:22 AM   #3
Carmen
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OK,
I will try

Thanks
Crm
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