User: saamar.rajput

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Posts by saamar.rajput

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SPIA error in DE-Colorectal
... Hey Adi, i have used spia a copule of time now and i never got this error before but just recently i am having this error, all my data looks very fine to me at every step but when i try running spia i get this error message.Although my DE-Colorectal has both the entrez ID and the logfoldchange in i ...
spia written 16 months ago by saamar.rajput0
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Error in TopologyGSA
... I am trying to run TopologyGSA function on my data to extract the pathways and i guess on the last step i get this error. Error in `[[<-.data.frame`(`*tmp*`, i, value = c(1L, 1L, 1L, 1L, 1L, 1L,  :   replacement has 33 rows, data has 1 I do not understand the error.Can somebody help? ...
dataframe topologygsa written 18 months ago by saamar.rajput0
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Comment: C: how to convert emsembl identiers with ENTERz ID in a logfoldchange files genera
... Thanks alot Michael :) ...
written 18 months ago by saamar.rajput0
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how to convert emsembl identiers with ENTERz ID in a logfoldchange files generated by DESeq2 to be used for SPIA
... I have a logfoldchange file generated using DESeq2 and I want to further used it for SPIA(pathways analysis). Spia requires 2 vectors to be passed as parameters "LogFoldChange" and "ENTERZ GENE ID". In my file I have ENSEMBL identifiers and logFoldChange. Either I have to add ENTERZ gene ID in an ex ...
deseq2 runspia enterz written 18 months ago by saamar.rajput0 • updated 18 months ago by Michael Love14k
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Normalized count or Count data for ToPASeq package
... Hi All, I am using the ToPASeq package for pathway analysis for my RNASe data for host and pathogen simultaneoulsy. I used htseq-counts to get the counts against each gene after mapping for both the host and pathogen RNASeq data. then I tried to merge the samples to make a count data file for the i ...
rnaseq topaseq written 18 months ago by saamar.rajput0

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