Geo2R troubleshooting

Question

[Sanjukta]

Hi. I have been working on Geo2R for the past few weeks. Since yesterday, it is displaying the following message. I am new to bioinfo and need help interpreting the message.

 Your request could not be completed. Below is the R output which might give you a hint about possible errors. You may also consult documentation on GEO2R Limitations and caveats.
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

===trying to list dir 
auto
ftp://ftp-ext.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161355/matrix/
Found 1 file(s)
GSE161355_series_matrix.txt.gz
===trying to download 
GSE161355_series_matrix.txt.gz
trying URL 'ftp://ftp-ext.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161355/matrix/GSE161355_series_matrix.txt.gz'
Content type 'unknown' length 7311872 bytes (7.0 MB)
==================================================
Error in .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim,  : 
  No residual degrees of freedom in linear model fits
Calls: eBayes -> .ebayes
Execution halted

Edit: I was analyzing GSE1297 dataset from the start. Right now, On grouping all the 9 control samples into CONTROL group and all the 7 Severe samples into SEVERE, Geo2R is displaying an error

Error: Your request could not be completed.

Where did I go wrong?

[GenoMax]

What exactly were you trying to do? You are using the online Geo2R interface? I just tried GSE161355 and was able to complete a basic two group comparison.

Answer 1

[mark.ziemann]

This sort of thing happens when you have too few samples per group. Ensure you have >2 per group and more if you are correcting for covariates like sex and age.

[ATpoint]

It is not necessarily related to sample size. It happens when you try to fit colinear models, for example Sex+Batch where Sex is nested by Batch.

[Sanjukta]

The error showed when we were taking one from each control and treated it to run the program. Also, as ATpoint has mentioned, the error showed when I ignored the sex differences in each group. Also a new error appears when the control group is larger than treated.

[ATpoint]

Basic rules of statistics: 1 vs 1 is invalid, and covariates must not be nested (=being the same) when including them in the same model.

[Sanjukta]

ATpoint I am getting an error message: "Your request could not be completed." on grouping all 7 and 9 samples into Severe and Control groups of GSE1297 dataset. What is your take?