Need help to get a DEseq or EdgeR example file

neetu · 12-02-2013, 07:13 AM

Hi,
I am a novice in RNA-seq data analysis.

I need a list of DEG from RNA-seq data. I need to test this list against some new workflows developed inhouse. Can anyone suggest how i can get such a list.

I tried GEO website and uploaded the files from the GSE44674 dataset.

GSE44674_DESeq_normalised_matrix_file_all_55_samples.txt.gz and
GSE44674_TKT-TMM-EDGER-NORM-55-SAMPLES.txt.gz

I presumed that since these are output files from EDGER and DEseq, they should have a list of DEG with p-values and log fold change.

On the contrary these files have columns for GO accession and columns for all 55 samples with values.

How can i find a list of DEG analyzed from RNA-seq data?
Any help in this direction will be very helpful.

Thanks and Regards,
Neetu

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12-02-2013, 07:13 AM	#1
neetu Member Location: India Join Date: Oct 2011 Posts: 11	Need help to get a DEseq or EdgeR example file Hi, I am a novice in RNA-seq data analysis. I need a list of DEG from RNA-seq data. I need to test this list against some new workflows developed inhouse. Can anyone suggest how i can get such a list. I tried GEO website and uploaded the files from the GSE44674 dataset. GSE44674_DESeq_normalised_matrix_file_all_55_samples.txt.gz and GSE44674_TKT-TMM-EDGER-NORM-55-SAMPLES.txt.gz I presumed that since these are output files from EDGER and DEseq, they should have a list of DEG with p-values and log fold change. On the contrary these files have columns for GO accession and columns for all 55 samples with values. How can i find a list of DEG analyzed from RNA-seq data? Any help in this direction will be very helpful. Thanks and Regards, Neetu