search

hmsiccbl / screensaver1

Screensaver Version 1 - End of life on December 1, 2018
GNU General Public License v2.0
3 stars 3 forks source link

Gene symbol in Dharmacon Human5 Pools: RefSeq27 Reversion library #116

Closed JenniferSplaine closed 10 years ago

JenniferSplaine commented 10 years ago

Sean

this is a fairly big issue not sure when it happened but for this library: Dharmacon Human5 Pools: RefSeq27 Reversion The gene symbol is returning as a date field. not sure when it got corrupted and this library is not screened that often but a screener just reported it.

Can you look into and fix asap thanks jen

JAS60 commented 10 years ago

Sean - just to reiterate, this is a really big issue! Thanks, Jen

JenniferSplaine commented 10 years ago

ok more info its the entrez Gene symbol field

and its not for every member of the library... here are the ones reported so far but i think you'll have to do a search to locate all of them

Plate 51008 Well H21 EG "Tue Aug 31 20:00:00 EDT 2010" Plate 51010 Well E10 EG "Tue Sep 07 20:00:00 EDT 2010" Plate 51012 Well C13 EG "Tue Mar 02 19:00:00 EST 2010" Plate 51018 Well G14 EG "Sun Feb 28 19:00:00 EST 2010" Plate 51019 Well I11 EG "Sat Mar 06 19:00:00 EST 2010"

i am offline for next hours dentist appt for callan but will be back by 1pm you can always send me a text to 603-765-6424 if its a question Jen

dwrobel1 commented 10 years ago

The problem is due to the symbols of some genes that appear as date names -- SEPT8 is an example. Excel converted to 8-Sep, and Screensaver interprets as a date. This could be corrected in the loading files if a Screensaver solution is not easy. -Dave

From: Jen Nale [notifications@github.com] Sent: Friday, October 04, 2013 10:42 AM To: hmsiccbl/screensaver Subject: Re: [screensaver] Gene symbol in Dharmacon Human5 Pools: RefSeq27 Reversion library (#116)

ok more info its the entrez Gene symbol field

and its not for every member of the library... here are the ones reported so far but i think you'll have to do a search to locate all of them

Plate 51008 Well H21 EG "Tue Aug 31 20:00:00 EDT 2010" Plate 51010 Well E10 EG "Tue Sep 07 20:00:00 EDT 2010" Plate 51012 Well C13 EG "Tue Mar 02 19:00:00 EST 2010" Plate 51018 Well G14 EG "Sun Feb 28 19:00:00 EST 2010" Plate 51019 Well I11 EG "Sat Mar 06 19:00:00 EST 2010"

i am offline for next hours dentist appt for callan but will be back by 1pm you can always send me a text to 603-765-6424 if its a question Jen

— Reply to this email directly or view it on https://github.com/hmsiccbl/screensaver/issues/116#issuecomment-25703729 GitHub.

seanderickson commented 10 years ago

The data will have to be reloaded - the conversion to a date value happened when the Excel file was saved, and so the values that were loaded into Screensaver were the actual date values.

(yet another example of the flakiness of the Excel file format)

dwrobel1 commented 10 years ago

There were 7 wells that had a date conversion problem in Human 5 pools. I've corrected and reloaded for this library, and will check all pool and duplex libraries to see if others have this problem (Mouse 5 pools looks like it needs to be corrected but others I checked were fine).

JAS60 commented 10 years ago

Thank you!!

JenniferSplaine commented 10 years ago

Thank you Sean and Dave! Dave is there anyway you can list all the wells in Human 5 that had this problem? So I can just send one list to Min Lui?

thanks

dwrobel1 commented 10 years ago

These are the wells I corrected:

51018 G14, MARCH1 51023 B15, MARCH2 51012 C13, MARCH3 51019 I11, MARCH7 51021 G19, MARCH8 51008 H21, SEPT1 51010 E10, SEPT8

From: Jen Nale [notifications@github.com] Sent: Friday, October 04, 2013 12:47 PM To: hmsiccbl/screensaver Cc: Wrobel, David J. Subject: Re: [screensaver] Gene symbol in Dharmacon Human5 Pools: RefSeq27 Reversion library (#116)

Thank you Sean and Dave! Dave is there anyway you can list all the wells in Human 5 that had this problem? So I can just send one list to Min Lui?

thanks

— Reply to this email directly or view it on https://github.com/hmsiccbl/screensaver/issues/116#issuecomment-25713334 GitHub.

JenniferSplaine commented 10 years ago

Thanks Dave! jeez can see why excel did that...