Closed davebridges closed 10 years ago
Also, the ../data/processed/RPKM_counts_Cushing_GRCh37.74.csv file has the acromegaly samples in it not the cushing's sample. We need to make that table with cushings samples as well. I am factoring out the barplots and heatmaps code into cushing_barplots, acromegaly_barplots etc, so make sure you do a pull before you start this.
OK found the RPKM file, sorry about that, i didnt notice you re-ordered it. I just need the VSD/RLD transformed files for Cushing.
I'm little bit confused. What do you need from me? Which files?
The files for Cushing are: VSD_DESeq2_Results-Cushing.csv and RLD_DESeq2_Results-Cushing.csv. Again, I forgot to put the issue number in the commit. Is this what you need? The files I used to generate these files named deseq_analysis_outlier_of_htseq.Rmd. I will clean the scripts folder to make things easier for us.
i need the cushings equivalent of the VSD RPKM table. For acromegaly its called ../data/processed/RPKM_VSD_counts_table_Acromegaly.csv
On Wed, Jun 4, 2014 at 5:25 PM, Quynh Tran notifications@github.com wrote:
The files for Cushing are: VSD_DESeq2_Results-Cushing.csv and RLD_DESeq2_Results-Cushing.csv. Again, I forgot to put the issue number in the commit. Is this what you need? The files I used to generate these files named deseq_analysis_outlier_of_htseq.Rmd. I will clean the scripts folder to make things easier for us.
— Reply to this email directly or view it on GitHub https://github.com/BridgesLab/CushingAcromegalyStudy/issues/26#issuecomment-45159968 .
The RPKM_VSD_counts_table_Cushing.csv is created.
I was trying to make heatmaps for Cushing's and i couldnt find the cushings files for this:
../data/processed/RPKM_VSD_counts_table_Acromegaly.csv
So I figured id just generate it for Cushing's but then I couldn't find the script where you made that file. It should be in either the DESeq or RPKM script right? I think you might have forgotten to merge it into master at some point.