User: mahm

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mahm20
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Posts by mahm

<prev • 29 results • page 1 of 3 • next >
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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 13 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 13 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 13 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$CellType) Design.mat <- model.matrix(~ ...
limma design matrix written 13 months ago by mahm20 • updated 11 months ago by Gordon Smyth39k
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Comment: C: Normalize the raw data from multiple studies
... Thanks. I will be careful from now. Yes, I know how to query from GSE files. I thought the same would be possible here too.   ...
written 13 months ago by mahm20
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Normalize the raw data from multiple studies
... I'm trying to normalize the data from multiple studies performed using same platform. ibrary(gcrma) library(limma) downloadedAffyFiles <- list.files(path = "GSE53454_RAW/", pattern = "CEL.gz$",full.names=TRUE) AffyData <- ReadAffy(filenames = downloadedAffyFiles) eset <- gcrma(AffyData) ...
normalization affy written 13 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 13 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 13 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 13 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 13 months ago by mahm20

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