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BridgesLab / CushingAcromegalyStudy

The source code for the cushing and acromegaly studies, currently ongoing
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Cant Find VSD RPKM Table Scripts #26

Closed davebridges closed 10 years ago

davebridges commented 10 years ago

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.

davebridges commented 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.

davebridges commented 10 years ago

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.

qtran1 commented 10 years ago

I'm little bit confused. What do you need from me? Which files?

qtran1 commented 10 years ago

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.

davebridges commented 10 years ago

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 .

qtran1 commented 10 years ago

The RPKM_VSD_counts_table_Cushing.csv is created.