# Residual standard error: 0.1187 on 55 degrees of freedom # Residual standard error: 0.1345 on 55 degrees of freedom See if any of the variables correlate with batch summary(lm(sva1$sv ~ pheno$batch)) # Response Y1 : Sva1 = sva(edata,mod,mod0,n.sv=2) # Number of significant surrogate variables is: 2 Here we won’t adjust for anything to see if sva can “discover” the batch effect. To do this, we need to build a model with any known adjustment variables and the variable we care about mod and another model with only the adjustment variables. Actually as written, those commands will act on all mounted volumes, but that should do no harm.First we need to estimate the surrogate variables.
They do not change any ownerships or change any permissions that should not normally be in effect anyway. With respect to the locked system volume in Target Disk Mode, I think it would be OK to run V.K.s Terminal commands. What about the contents of the disk? Can you access everything? Are there any folders there with red "no entry " badges? At this point, though, you have a functioning system and it might well be prudent to leave well enough alone. I don't know if such an access "patch" could somehow increase the chance of some problem down the road, which might be avoided if instead you correct the ordinary permissions to what they should be, obviating the need for the ACL. WORKED! I'm back in!Ĭommand again, you will likely find that the previously messed-up ownership and permissions are still messed-up, and that there is now a new ACL that overrides them, giving you access. So, he had me just unlock it, hit the plus button, and add my username. Then assuming from your Terminal posting that your current admin username is "leahnlaw", I would set up BatChmod this way and click Apply:
To do this, you could drag the icon of the volume in question into BatChmod's field to the right of "File.". I would try first just on the volume itself, without checking the box for "Apply to enclosed folders and files." I think it is OK to try BatChmod as you had planned. With regard to the zero K size, that might be just a consequence of your lack of permission to read/search the volume - we don't know yet what is actually there. Well, I'm not a Unix expert, but I see a number of problems-ġ) There is a strange ACL - I don't know where the long string "40C0." came from.Ģ) No one has directory "search" permission (the x-bit is not set)ģ) The owner and group owner are listed by number (502) rather than by name, which means that there is currently no user or group with those UID/GID numbers.
Lawrence-Ingrams-Mac-Pro:~ leahnlaw$ ls /Volumes/Archiveĭrw-rw-r-+ 19 502 502 - 714 Apr 20 12:43 /Volumes/ArchiveĠ: 40C0F312-42F5-4FCF-9D28-A2D91B031ED7 allow list,add_file,add_subdirectory,readattr,writeattr,readextattr,writeextattr,read security
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