User: mahm

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mahm20
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Posts by mahm

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Querying concentration of a species using hmdbquery
... Hi All, I am using hmdbquery to filter the concentration of some of the metabolites documented in HMDB. I'm referring to the hmdbquery manual that is available here . I'm facing challenge in finding the appropriate command that has to be used to parse the normal concentration of the species ,HMDB0 ...
metabolitedata hmdb hmdbquery written 6 months ago by mahm20
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Comment: C: Using eset while parsing GSE file located in a path
... Hi, This the output of df -h Filesystem Size Used Avail Use% Mounted on udev 3.9G 0 3.9G 0% /dev tmpfs 787M 9.5M 777M 2% /run /dev/sda4 97G 12G 81G 13% / tmpfs 3.9G 7.5M 3.9G 1% /dev/shm tmpfs 5.0M 4.0K 5.0M 1% /run/lock ...
written 6 months ago by mahm20
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Comment: C: Using eset while parsing GSE file located in a path
...   /media/nat is a directory on  my laptop. Type(inode/directory) .I have full read and write permissions at that location. It has a total capacity of 212 GB and used is 20GB. > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS ...
written 6 months ago by mahm20
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Creating a design matrix
... I'm creating a design matrix as follows, library(gcrma) library(limma) gseEset <- getGEO('GSE20966')[[1]] DesignMatrixInput <- pData(gseEset)[,45,drop=FALSE] colnames(DesignMatrixInput)[1] <- "CellType" CellTypeLabel <- unique(DesignMatrixLabel$CellType) Design.mat <- model.matrix(~ ...
limma design matrix written 6 months ago by mahm20 • updated 4 months ago by Gordon Smyth36k
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Comment: C: Normalize the raw data from multiple studies
... Thanks. I will be careful from now. Yes, I know how to query from GSE files. I thought the same would be possible here too.   ...
written 6 months ago by mahm20
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Normalize the raw data from multiple studies
... I'm trying to normalize the data from multiple studies performed using same platform. ibrary(gcrma) library(limma) downloadedAffyFiles <- list.files(path = "GSE53454_RAW/", pattern = "CEL.gz$",full.names=TRUE) AffyData <- ReadAffy(filenames = downloadedAffyFiles) eset <- gcrma(AffyData) ...
normalization affy written 6 months ago by mahm20
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Comment: C: Using Limma to normalize data sets
... Fixed things!! Works perfect. Thanks a lot for the tremendous support! ...
written 6 months ago by mahm20
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Comment: C: Using Limma to normalize data sets
... I'm updated to R version 3.5.1 (2018-07-02) and Bioconductor 3.7.Now, I find this error eset <- gcrma(AffyData) Adjusting for optical effect..........................................................................................Done. Computing affinities[1] "Checking to see if your internet co ...
written 6 months ago by mahm20
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Comment: C: Using Limma to normalize data sets
... The files are in the current working directory. Also, GSM1293830_19_10_Control_108h.CE was displayed in the terminal.The file in with the correct extension in the directory.Now ,I get a status that reads "Adjusting for non-specific binding.Killed" ? Is something wrong? AffyBatch object size of arr ...
written 6 months ago by mahm20
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Comment: C: Using Limma to normalize data sets
... I tried as you suggested, The following error appears :( > downloadedAffyFiles <- list.files(path = "../Data/GSE53454_RAW", pattern = "CEL.gz$") > AffyData <- ReadAffy(filenames = downloadedAffyFiles) Error: the following are not valid files:     GSM1293805_10_4_Control_0h.CEL.gz    GS ...
written 6 months ago by mahm20

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