User: tanyabioinfo

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tanyabioinfo10
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Posts by tanyabioinfo

<prev • 21 results • page 1 of 3 • next >
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Comment: A: RNA seq tximport
... Hi Michael   Thanks a lot. My TPM data is showing a lot of variation in terms of trends than RPM. Like the tximport output gives a lot of  variation among the replicates. Can you please help me why this would be happening.   Thanks   Tanya ...
written 19 days ago by tanyabioinfo10
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RNA seq tximport
... Hi I am using Salmon to process my RNA seq data. I just want to confirm that the abundance given as an output by the tximport package corresponds to TPM. Many of the cells (the output of tximport) have a value of zero which is making me think about this. Regards Tanya ...
tximport written 21 days ago by tanyabioinfo10
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tximport gene name
... Hi I am doing the following to get the tximport count  matrix with gene name in the first column txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame") txdf$symbol <- mapIds(EnsDb.Mmusculus.v79, txdf$gene_id, "GENENAME", "GENEID") tx2gene <- as.data.frame(txdf[,c("tx_id","sym ...
tximport written 27 days ago by tanyabioinfo10 • updated 22 days ago by Ed Siefker210
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Comment: A: PCA from TPM
... Hi Michael I am now using the follwoing code: txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE) sampleTable <- data.frame(condition =samples$condition,time=factor(samples$time)) rownames(sampleTable) <- colnames(txi$counts) dds <- DESeqDataSe ...
written 27 days ago by tanyabioinfo10
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PCA from TPM
... Hi I am trying to do PCA analysis of my samples. I generated the matrix using the tximport package. I have transcript ids as my rows and the sample names are the columns. txi <- tximport(files, type="salmon", tx2gene=NULL, ignoreTxVersion=TRUE,dropInfReps=TRUE,txOut = TRUE) tpm <- (txi$abun ...
pca tpm tximport written 28 days ago by tanyabioinfo10
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Answer: A: RNA seq tximport
... Thanks James It worked for me.   ...
written 28 days ago by tanyabioinfo10
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RNA seq tximport
... Hi   I am using the following commands to run tximport txi <- tximport(files, type="salmon", tx2gene=tx2gene,ignoreTxVersion=TRUE,dropInfReps=TRUE) my tx2gene dataframe looks like this              tx_id            gene_id 1 ENSMUST00000082387 ENSMUSG00000064336 2 ENSMUST00000179436 ENSMUSG0 ...
tximport written 28 days ago by tanyabioinfo10
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Comment: C: PCA plot for TPM data
... Thanks Andy. Can you please help me how can I add colors to this PCA plot based on sample names.   Thanks   Tanya ...
written 29 days ago by tanyabioinfo10
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PCA plot for TPM data
... Hi I am having a TPM count matrix. The columns are the samples wt0hr wt6hr wt24hr kd0hr kd6hr kd24 and have four replicates for each one of them. Can some one help me with the correct R package to plot the PCA for samples when I have the TPM data.   Thanks Tanya ...
pca written 29 days ago by tanyabioinfo10 • updated 29 days ago by Andy9130
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Answer: A: Heat MAP TPM
... Thanks Chris   I did that and it works fine for me. So now the R script looks like this: logTransformed.dat = log2(counts_filtered_df + 1) z.mat <- t(scale(t(logTransformed.dat), scale=TRUE, center=TRUE)) heatmap.2(z.mat, dendrogram="both", scale="none", trace="none") I have one more questio ...
written 29 days ago by tanyabioinfo10

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