degCheckFactors error

[maria-xi]

Hi, I'm trying to run DEGreport following this tutorial http://bioconductor.org/packages/devel/bioc/vignettes/DEGreport/inst/doc/DEGreport.html. I have installed and loaded DEGreport 1.18.1.
when I try to run " degCheckFactors(counts[, 1:6])", I keep getting the following error:
Error in degCheckFactors(normalized_counts[, 1:6]) :
could not find function "degCheckFactors"
I have tried re-installing and loading the package again and again but I keep getting the same issue. Any ideas what could have gone wrong?

[lpantano]

Hi,

sorry about this.

Can you do this and tell me the output.

open a new R session and type:

library(DEGreport)
data(humanGender)
library(SummarizedExperiment)
degCheckFactors(assays(humanGender)[[1]][, 1:10])

Does this work or you get the same error?

if this gets an error can you send me the output of sessionInfo()

Thanks!

[maria-xi]

Thanks for getting back to me so quickly. When I opened a new session and only wrote the commands you provided, it worked fine. I guess it's one of the other packages I have loaded in my session that interferes with this one. Any ideas how to troubleshoot for that? Or what packages could be interfering? Thanks, again

…

On Mon, Jan 7, 2019 at 4:05 PM Lorena Pantano ***@***.***> wrote: Hi, sorry about this. Can you do this and tell me the output. open a new R session and type: library(DEGreport) data(humanGender) library(SummarizedExperiment) degCheckFactors(assays(humanGender)[[1]][, 1:10]) Does this work or you get the same error? if this gets an error can you send me the output of sessionInfo() Thanks! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AqryzZrrzescnb1onCc5eVoh0zYcLfMxks5vA7aKgaJpZM4Z0SRB> .

[maria-xi]

Not sure what the issue was but it is now working fine in my previous session with all other packages. Thanks for your help! On Mon, Jan 7, 2019 at 4:50 PM Ximena Sosa <[email protected]> wrote:

…

Thanks for getting back to me so quickly. When I opened a new session and only wrote the commands you provided, it worked fine. I guess it's one of the other packages I have loaded in my session that interferes with this one. Any ideas how to troubleshoot for that? Or what packages could be interfering? Thanks, again On Mon, Jan 7, 2019 at 4:05 PM Lorena Pantano ***@***.***> wrote: > Hi, > > sorry about this. > > Can you do this and tell me the output. > > open a new R session and type: > > library(DEGreport) > data(humanGender) > library(SummarizedExperiment) > degCheckFactors(assays(humanGender)[[1]][, 1:10]) > > Does this work or you get the same error? > > if this gets an error can you send me the output of sessionInfo() > > Thanks! > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#23 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AqryzZrrzescnb1onCc5eVoh0zYcLfMxks5vA7aKgaJpZM4Z0SRB> > . >

[lpantano]

Glad that it worked. Sometimes sessions mess up with old-new loaded packages. Cheers Lorena Pantano, P.h.D Research Scientist Biostatistics Department Harvard T.H. Chan School of Public Health https://mirtop.github.io https://lpantano.github.io I'll be out of office from Dec-17th to Jan9th

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On Mon, Jan 7, 2019 at 5:09 PM maria-xi ***@***.***> wrote: Not sure what the issue was but it is now working fine in my previous session with all other packages. Thanks for your help! On Mon, Jan 7, 2019 at 4:50 PM Ximena Sosa ***@***.***> wrote: > Thanks for getting back to me so quickly. > > When I opened a new session and only wrote the commands you provided, it > worked fine. I guess it's one of the other packages I have loaded in my > session that interferes with this one. Any ideas how to troubleshoot for > that? Or what packages could be interfering? > > Thanks, again > > On Mon, Jan 7, 2019 at 4:05 PM Lorena Pantano ***@***.***> > wrote: > >> Hi, >> >> sorry about this. >> >> Can you do this and tell me the output. >> >> open a new R session and type: >> >> library(DEGreport) >> data(humanGender) >> library(SummarizedExperiment) >> degCheckFactors(assays(humanGender)[[1]][, 1:10]) >> >> Does this work or you get the same error? >> >> if this gets an error can you send me the output of sessionInfo() >> >> Thanks! >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> <#23 (comment) >, >> or mute the thread >> < https://github.com/notifications/unsubscribe-auth/AqryzZrrzescnb1onCc5eVoh0zYcLfMxks5vA7aKgaJpZM4Z0SRB > >> . >> > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HC7XflMnHgWWaw53iAsqgsdkJaVWks5vA8V8gaJpZM4Z0SRB> .