Open meichendong opened 5 years ago
Hi meichendong,
At the moment,this $new() constructor can take matrix and data.frame as an input (as a first argument, instead of character GEO identifier)
Basically
lo <- LinseedObject$new(matrixObject, samples=1:10, topGenes=10000)
should work just fine.
But if you pass the dataset by yourself, make sure your data is normalized (quantile for microarrays and something like RPKMs for RNA-seq data).
I won't close this issue until I write better documentation for the initialization method.
Cheers, Konstantin
oops. I think this is the question I asked. I will try to make a linseed object with a matrix of the RPKM for the set. The original idea was to collect differential expression with a relative comparison model. so we have treatment samples and control samples, both heterogeneous. They were prepared the same way, so they should have a similar mixture of cells. However, there could be something about the treatment which could cause cells to differentiate. I was thinking of doing each separately and then potentially comparing the deconvoluted gene expression from similar unmixed populations. A tutorial for this would be very helpful.
Can we also use DESeq normalized data for this?
Hi,
I am trying to work on the deconvolution of expression data and found this package very helpful. However, when l tried to specify GEO accession number, l encountered an error.
Found 1 file(s)
GSE14641_series_matrix.txt.gz
Using locally cached version: /var/folders/3t/9lv4qds57kvg31f9zsxdr_zm0000gn/T//RtmpN2ajN6/GSE14641_series_matrix.txt.gz
Annotation GPL not available, so will use submitter GPL instead
Using locally cached version of GPL8132 found here:
/var/folders/3t/9lv4qds57kvg31f9zsxdr_zm0000gn/T//RtmpN2ajN6/GPL8132.soft.gz
Error in [.data.frame
(annotation, , geneSymbol, drop = FALSE) :
undefined columns selected
It seems this error is associated with the input file. As per the previous discussion with #1 l should specify object file rather than GEO accession number.
Is there any manual available on how to create an input object file using the GEO database, any tool recommendation?
Raj
Hi I was wondering if you can give more details about how to create the LinseedObject? While I was trying to use the public data GSE50244, I ended up with error like:
> lo <- LinseedObject$new("GSE50244", samples=1:10, topGenes=10000) Found 1 file(s) GSE50244_series_matrix.txt.gz Using locally cached version: C:\Users\meichen\AppData\Local\Temp\RtmpiWoz2m/GSE50244_series_matrix.txt.gz Parsed with column specification: cols( .default = col_character() ) See spec(...) for full column specifications. Annotation GPL not available, so will use submitter GPL instead Using locally cached version of GPL11154 found here: C:\Users\meichen\AppData\Local\Temp\RtmpiWoz2m/GPL11154.soft Error in if (qx[5] - qx[1] > 100 || qx[5] > 100) { : missing value where TRUE/FALSE needed In addition: Warning message: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL11nnn/GPL11154/annot/GPL11154.annot.gz': HTTP status was '404 Not Found'
I was wondering is there another way to create an object? Like simply using the expression matrix or an expressionSet object?
Thanks!