new to RNASeq

Navi · 06-09-2011, 07:21 AM

Hello everyone,

I want to analyze my RNASeq data using DESeq. Would anyone tell me how and where to find codes for DESeq? I'm naive to DESeq. Thx

KellerMac · 06-09-2011, 08:17 AM

On the bioconductor webpage there is a pdf file you can download that runs through analyzing data with deseq. Its not that hard, and you can copy and paste commands directly from the pdf to the R interface.

Navi · 06-09-2011, 09:30 AM

Thanks KellerMac for the quick response. I got a pdf for DESeq. I want to compare WT with mutant with no replication. I am not getting the codes. Which codes should I use to compare WT with mutants? I'm interested in over-represented genes in both WT and mutant?

KellerMac · 06-10-2011, 08:40 AM

start out with section two "preparations" and import your data from a text or exel file into "r" it can be a little tricky my command looked like this exampleFile = "/Users/ck_lab_5/Desktop/LowInputSAGE/LIS_RAW1.tab.txt" once youve done that you need to set "conditions" which basically splits your data into two sets based on experimental factors i.e. WT and Mutant. i suggest following the protocol to normalize your data and loose sets that are too variable as this will skew your results (look at the ECDF plots) section four contains the commands to get differential expression data. Just make sure you change their conditions to yours ( they use T and N whereas I used "a" and "b")

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06-09-2011, 07:21 AM	#1
Navi Junior Member Location: midwest Join Date: Jun 2011 Posts: 6	new to RNASeq Hello everyone, I want to analyze my RNASeq data using DESeq. Would anyone tell me how and where to find codes for DESeq? I'm naive to DESeq. Thx

06-09-2011, 08:17 AM	#2
KellerMac Member Location: Baton Rouge, Louisiana Join Date: Jun 2011 Posts: 11	On the bioconductor webpage there is a pdf file you can download that runs through analyzing data with deseq. Its not that hard, and you can copy and paste commands directly from the pdf to the R interface.

06-09-2011, 09:30 AM	#3
Navi Junior Member Location: midwest Join Date: Jun 2011 Posts: 6	Thanks KellerMac for the quick response. I got a pdf for DESeq. I want to compare WT with mutant with no replication. I am not getting the codes. Which codes should I use to compare WT with mutants? I'm interested in over-represented genes in both WT and mutant?

06-10-2011, 08:40 AM	#4
KellerMac Member Location: Baton Rouge, Louisiana Join Date: Jun 2011 Posts: 11	start out with section two "preparations" and import your data from a text or exel file into "r" it can be a little tricky my command looked like this exampleFile = "/Users/ck_lab_5/Desktop/LowInputSAGE/LIS_RAW1.tab.txt" once youve done that you need to set "conditions" which basically splits your data into two sets based on experimental factors i.e. WT and Mutant. i suggest following the protocol to normalize your data and loose sets that are too variable as this will skew your results (look at the ECDF plots) section four contains the commands to get differential expression data. Just make sure you change their conditions to yours ( they use T and N whereas I used "a" and "b")