DESeq - Error: More than one fitInfo object available.

tikacp · 02-18-2013, 03:30 AM

hello,

i was trying out different methods to estimate the dispersions in my data and ran into the following problem for the 'per-condition' method ('blind' and 'pooled' work fine):

Code:

> cds <- newCountDataSet(exprs(dataNormGC),data$virtual_conditions)
> sizeFactors(cds) <- rep(1,18)
> cds <- estimateDispersions(cds,method="per-condition",sharingMode="maximum")
> plotDispEsts(cds)
Error in fitInfo(cds, name = name) : 
  More than one fitInfo object available. Specify by name. (See 'ls(cds@fitInfo)' for a list.)
Calls: plotDispEsts -> fitInfo

as suggested, i looked into

Code:

> ls(cds@fitInfo)

which only said

Code:

[1] "pooled"

can anyone explain to me why that happens?
in case it is important: my data contains replicates only for some conditions, not for all.

thanks
tim

mdarby · 06-06-2013, 02:57 PM

I am getting this same error. My data contains replicates for all conditions. Did you find an answer?

tikacp · 06-10-2013, 02:55 AM

hi,

unfortunately, i haven't found any solution, yet. i thought that maybe something attached to the workspace would cause the problem, but that wasn't it, either. i don't know where else to look currently, sorry.

cheers
tim

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
DESeq error	clemen	Bioinformatics	22	03-27-2014 05:59 AM
DESeq error	Carmen	Bioinformatics	2	01-17-2013 06:22 AM
Cuffmerge command giving error- TypeError: 'str' object is not callable	kumardeep	RNA Sequencing	1	05-21-2012 05:21 AM
DESeq Plot Error	coralgirl	Bioinformatics	2	11-29-2011 10:35 AM
[DESeq] invalid class "CountDataSet" object	Azazel	Bioinformatics	4	11-08-2011 01:34 AM

02-18-2013, 03:30 AM	#1
tikacp Junior Member Location: Greifswald Join Date: Feb 2013 Posts: 2	DESeq - Error: More than one fitInfo object available. hello, i was trying out different methods to estimate the dispersions in my data and ran into the following problem for the 'per-condition' method ('blind' and 'pooled' work fine): Code: > cds <- newCountDataSet(exprs(dataNormGC),data$virtual_conditions) > sizeFactors(cds) <- rep(1,18) > cds <- estimateDispersions(cds,method="per-condition",sharingMode="maximum") > plotDispEsts(cds) Error in fitInfo(cds, name = name) : More than one fitInfo object available. Specify by name. (See 'ls(cds@fitInfo)' for a list.) Calls: plotDispEsts -> fitInfo as suggested, i looked into Code: > ls(cds@fitInfo) which only said Code: [1] "pooled" can anyone explain to me why that happens? in case it is important: my data contains replicates only for some conditions, not for all. thanks tim

06-06-2013, 02:57 PM	#2
mdarby Junior Member Location: Baltimore Join Date: Jun 2013 Posts: 1	I am getting this same error. My data contains replicates for all conditions. Did you find an answer?

06-10-2013, 02:55 AM	#3
tikacp Junior Member Location: Greifswald Join Date: Feb 2013 Posts: 2	hi, unfortunately, i haven't found any solution, yet. i thought that maybe something attached to the workspace would cause the problem, but that wasn't it, either. i don't know where else to look currently, sorry. cheers tim