Functional analysis error

[Former user]

miARma-Seq calls an error at the functional analysis start stating that the logfiles are not present although I can see them to be present in my output directory.

Cees

F_Analysis ERROR :: [Thu Aug 17 11:50:50 2017] projectdir(/Users/ceesoudejans/Desktop/miARna_output), up(HASH(0x7f98d9e40298)), down(), universe(HASH(0x7f98da08c378)), organism(human), logfile (/Users/ceesoudejans/Desktop/miARna_output/miARma_logfile.927.log) have not been provided at /Users/ceesoudejans/Desktop/miARma1.7.0/lib/CbBio/RNASeq/FAnalysis.pm line 432.

[Eduardo Andres Leon]

Hi Cees, I see different strange things in your log files. 1) For example the % of counted reads is around 7% .... Are you sure that you experiment is forwarded ? I recommend you to use a different ini file including only the general and the Readcount sections and modifying the strand=yes parameter until you find a normal % (> 60-70%).

2) Then regarding the F_Analysis ... I have some suspicious but I'll need more information ... could you include the ini file?

Regards

[Cees Oudejans]

Hi Eduardo,

I managed to get the program running till the end. But the functional analysis is not done (less that 50 calls) despite the fact that the edgeR output gives 486 DE genes (FDR < 0.05).

Cees

[Cees Oudejans]

Hi Eduardo,

By the way, I was only able to finish till the end when desoft was limited to Edger. When combined with Doiseq, I get a conflict in R (version 3.4.1) with a failure to print the results.

Cees

[Eduardo Andres Leon]

Could you send me your ini file ?

Edu