Dear Sir, I am a bioinformatics master student doing some differential expression of gene in a wild type and mutated N. crassa. I came across the DEseq and want to use it in R doing my analysis to find differential expression and p-values. I have my read counts in an excel file which I converted to a text file. I loaded the file but not able to assign row to the genes and columns to different mutants and wild type. Can you please provide me a guide on how to get this analysis done starting from the excel file which have the read, and also do help me with user guide to follow if you have any available. Kind regards, Saikou Y Bah.Me Sybah2 [[alternative HTML version deleted]]

Dear Saikou On 02/05/2012 02:03 PM, saikouy bah wrote: > I am a bioinformatics master student doing some differential expression > of gene in a wild type and mutated N. crassa. I came across the DEseq > and want to use it in R doing my analysis to find differential > expression and p-values. I have my read counts in an excel file which I > converted to a text file. I loaded the file but not able to assign row > to the genes and columns to different mutants and wild type. Can you > please provide me a guide on how to get this analysis done starting from > the excel file which have the read, and also do help me with user guide > to follow if you have any available. The DESeq vignette (make sure you read the current version) gives an example of such a text file and shows how to read it in. Compare whether your text file has the same format and then follow the instructions. If you still cannot get it to work, please post an excerpt from your text file, the precise commands you have tried, and the output of 'sessionInfo()'. Simon

Please submit your R code so someone can help you to correct it. Regards, Naomi At 08:03 AM 2/5/2012, saikouy bah wrote: >Dear Sir, >I am a bioinformatics master student doing some differential expression >of gene in a wild type and mutated N. crassa. I came across the DEseq >and want to use it in R doing my analysis to find differential >expression and p-values. I have my read counts in an excel file which I >converted to a text file. I loaded the file but not able to assign row >to the genes and columns to different mutants and wild type. Can you >please provide me a guide on how to get this analysis done starting from >the excel file which have the read, and also do help me with user guide >to follow if you have any available. >Kind regards, >Saikou Y Bah.Me Sybah2 > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor