riazn / bms038_analysis Goto Github PK

This file is missing.

Thank you.

I'm trying to recreate this table and I think there is an error when intersecting the input matrix with the reference database.

Here is the section in question (lines 87-109):

# Read in matrix and Sample annotation
mat <- read.delim("data/CountData.BMS038.txt")
SampleTableCorrected <- read.csv("data/SampleTableCorrected.9.19.16.csv", row.names=1)

# Only samples with response
SampleTableCorrected <- SampleTableCorrected[!(is.na(SampleTableCorrected$Response)), ]

# Find the overlapping samples
inter <- intersect(colnames(mat),rownames(SampleTableCorrected))
SampleTableCorrected <- SampleTableCorrected[inter,]
mat <- mat[,match(rownames(SampleTableCorrected),colnames(mat))]

# Create the DESeq2 object
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
ebg <- exonsBy(txdb, by="gene")
intersection <- intersect(rownames(mat),ebg@partitioning@NAMES)
ebg2 <- ebg[ebg@partitioning@NAMES %in% intersection]

# sort by ID
ebg2 <- ebg2[order(names(ebg2))]

# Sort by gene model order
mat <- mat[match(names(ebg2), rownames(mat)),]

mat is initially read in as a data.frame with 22,333 rows (genes) and 120 columns (samples).

mat gets intersected with the samples in SampleTableCorrected to remove 15 samples, resulting in 22,333 rows and 103 columns (both the "ID" column and the "HUGO" column are also removed here).

ebg is created from txdb, which contains 23,459 elements.

The entrez IDs of ebg (ebg@partitioning@NAMES) are intersected with the rownames of mat, but the rownames of mat are just 1:nrow(mat):

intersection1 <- intersect(rownames(mat), ebg@partitioning@NAMES)
intersection2 <- intersect(as.character(1:nrow(mat)), ebg@partitioning@NAMES)
length(which(intersection1 != intersection2))
0

This intersection results in a mat with 7,866 rows and 103 columns. If the rownames of mat are instead changed to the original entrez IDs, we get a larger intersection:

# Read in matrix and Sample annotation
mat <- read.delim("data/CountData.BMS038.txt")
ids <- mat$ID
SampleTableCorrected <- read.csv("data/SampleTableCorrected.9.19.16.csv", row.names=1)

# Only samples with response
SampleTableCorrected <- SampleTableCorrected[!(is.na(SampleTableCorrected$Response)), ]

# Find the overlapping samples
inter <- intersect(colnames(mat),rownames(SampleTableCorrected))
SampleTableCorrected <- SampleTableCorrected[inter,]
mat <- mat[,match(rownames(SampleTableCorrected),colnames(mat))]
rownames(mat) <- ids

# Create the DESeq2 object
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
ebg <- exonsBy(txdb, by="gene")
intersection <- intersect(rownames(mat),ebg@partitioning@NAMES)
ebg2 <- ebg[ebg@partitioning@NAMES %in% intersection]

# sort by ID
ebg2 <- ebg2[order(names(ebg2))]

# Sort by gene model order
mat <- mat[match(names(ebg2), rownames(mat)),]

This results in a matrix with 22,333 genes and 103 samples. Although neither method above created the same results as were found in TableS6.A downloaded from the manuscript page.

In order to get an output table, I had to change: Response.ihw.PRCR <- ResFiltered(results(dds.pre,name="ResponsePRCR",filterFun = ihw)) to Response.ihw.PRCR <- ResFiltered(results(dds.pre,name="Response_PRCR_vs_PD",filterFun = ihw)), which may be the result of a different version of DESeq2 (I'm using 1.20.0).

Hi,

Thanks for making the code available and so user friendly. Great study.

For some reason, when I run TableS6.C.R I don't get the same results as those provided in Table S6C of the paper. The output I get is attached here.

Would be very helpful to get your feedback.

Thanks!
TableS6.xlsx

I was expecting to find the PD-L1 score by IHC in bms038_clinical_data.csv or a similar file with clinical data (e.g., Table S2. Clinical Characteristics, Related to Figure 1 (mmc2.csv); SampleTableCorrected_9_19_16.csv) from the code but have been unable to do so. Where can I find the PD-L1 score by PD-L1 for each patient? Thanks.

Could you please upload the "on_therapy_nonsynonmous_mutations.csv" file?

Thanks for making data and code available.

I try to use the website but Vivaldi is preventing me from accessing to an insecure site.